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Danos P, Giannoni‐Luza S, Murillo Carrasco AG, Acosta O, Guevara‐Fujita ML, Cotrina Concha JM, Guerra Miller H, Pinto Oblitas J, Aguilar Cartagena A, Araujo JM, Fujita R, Buleje Sono JL. Promoter hypermethylation of RARB and GSTP1 genes in plasma cell-free DNA as breast cancer biomarkers in Peruvian women. Mol Genet Genomic Med 2023; 11:e2260. [PMID: 37548362 PMCID: PMC10724513 DOI: 10.1002/mgg3.2260] [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: 04/07/2022] [Revised: 04/30/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Promoter hypermethylation is one of the enabling mechanisms of hallmarks of cancer. Tumor suppressor genes like RARB and GSTP1 have been reported as hypermethylated in breast cancer tumors compared with normal tissues in several populations. This case-control study aimed to determine the association between the promoter methylation ratio (PMR) of RARB and GSTP1 genes (separately and as a group) with breast cancer and its clinical-pathological variables in Peruvian patients, using a liquid biopsy approach. METHODS A total of 58 breast cancer patients and 58 healthy controls, matched by age, participated in the study. We exacted cell-free DNA (cfDNA) from blood plasma and converted it by bisulfite salts. Methylight PCR was performed to obtain the PMR value of the studied genes. We determined the association between PMR and breast cancer, in addition to other clinicopathological variables. The sensitivity and specificity of the PMR of these genes were obtained. RESULTS A significant association was not found between breast cancer and the RARB PMR (OR = 1.90; 95% CI [0.62-6.18]; p = 0.210) or the GSTP1 PMR (OR = 6.57; 95% CI [0.75-307.66]; p = 0.114). The combination of the RARB + GSTP1 PMR was associated with breast cancer (OR = 2.81; 95% CI [1.02-8.22]; p = 0.026), controls under 50 years old (p = 0.048), patients older than 50 (p = 0.007), and postmenopausal (p = 0.034). The PMR of both genes showed a specificity of 86.21% and a sensitivity of 31.03%. CONCLUSION Promoter hypermethylation of RARB + GSTP1 genes is associated with breast cancer, older age, and postmenopausal Peruvian patients. The methylated promoter of the RARB + GSTP1 genes needs further validation to be used as a biomarker for liquid biopsy and as a recommendation criterion for additional tests in asymptomatic women younger than 50 years.
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Affiliation(s)
- Pierina Danos
- Centro de Genética y Biología MolecularUniversidad de San Martín de PorresLimaPeru
| | | | | | - Oscar Acosta
- Facultad de Medicina HumanaUniversidad de San Martín de PorresChiclayoPeru
- Facultad de Farmacia y BioquímicaUniversidad Nacional Mayor de San MarcosLimaPeru
| | | | | | | | | | | | | | - Ricardo Fujita
- Centro de Genética y Biología MolecularUniversidad de San Martín de PorresLimaPeru
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2
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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3
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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Janssen LM, Suelmann BBM, Elias SG, Janse MHA, van Diest PJ, van der Wall E, Gilhuijs KGA. Improving prediction of response to neoadjuvant treatment in patients with breast cancer by combining liquid biopsies with multiparametric MRI: protocol of the LIMA study - a multicentre prospective observational cohort study. BMJ Open 2022; 12:e061334. [PMID: 36127090 PMCID: PMC9490628 DOI: 10.1136/bmjopen-2022-061334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The response to neoadjuvant chemotherapy (NAC) in breast cancer has important prognostic implications. Dynamic prediction of tumour regression by NAC may allow for adaption of the treatment plan before completion, or even before the start of treatment. Such predictions may help prevent overtreatment and related toxicity and correct for undertreatment with ineffective regimens. Current imaging methods are not able to fully predict the efficacy of NAC. To successfully improve response prediction, tumour biology and heterogeneity as well as treatment-induced changes have to be considered. In the LIMA study, multiparametric MRI will be combined with liquid biopsies. In addition to conventional clinical and pathological information, these methods may give complementary information at multiple time points during treatment. AIM To combine multiparametric MRI and liquid biopsies in patients with breast cancer to predict residual cancer burden (RCB) after NAC, in adjunct to standard clinico-pathological information. Predictions will be made before the start of NAC, approximately halfway during treatment and after completion of NAC. METHODS In this multicentre prospective observational study we aim to enrol 100 patients. Multiparametric MRI will be performed prior to NAC, approximately halfway and after completion of NAC. Liquid biopsies will be obtained immediately prior to every cycle of chemotherapy and after completion of NAC. The primary endpoint is RCB in the surgical resection specimen following NAC. Collected data will primarily be analysed using multivariable techniques such as penalised regression techniques. ETHICS AND DISSEMINATION Medical Research Ethics Committee Utrecht has approved this study (NL67308.041.19). Informed consent will be obtained from each participant. All data are anonymised before publication. The findings of this study will be submitted to international peer-reviewed journals. TRIAL REGISTRATION NUMBER NCT04223492.
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Affiliation(s)
- Liselore M Janssen
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Britt B M Suelmann
- Department of Medical Oncology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Markus H A Janse
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elsken van der Wall
- Department of Medical Oncology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kenneth G A Gilhuijs
- Image Sciences Institute, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
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5
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Kramer CJH, Vreeswijk MPG, Thijssen B, Bosse T, Wesseling J. Beyond the snapshot: optimizing prognostication and prediction by moving from fixed to functional multidimensional cancer pathology. J Pathol 2022; 257:403-412. [PMID: 35438188 PMCID: PMC9324156 DOI: 10.1002/path.5915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/10/2022]
Abstract
The role of pathology in patient management has evolved over time from the retrospective review of cells, tissue, and disease (‘what happened’) to a prospective outlook (‘what will happen’). Examination of a static, two‐dimensional hematoxylin and eosin (H&E)‐stained tissue slide has traditionally been the pathologist's primary task, but novel ancillary techniques enabled by technological breakthroughs have supported pathologists in their increasing ability to predict disease status and behaviour. Nevertheless, the informational limits of 2D, fixed tissue are now being reached and technological innovation is urgently needed to ensure that our understanding of disease entities continues to support improved individualized treatment options. Here we review pioneering work currently underway in the field of cancer pathology that has the potential to capture information beyond the current basic snapshot. A selection of exciting new technologies is discussed that promise to facilitate integration of the functional and multidimensional (space and time) information needed to optimize the prognostic and predictive value of cancer pathology. Learning how to analyse, interpret, and apply the wealth of data acquired by these new approaches will challenge the knowledge and skills of the pathology community. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- C J H Kramer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - M P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - B Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - T Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - J Wesseling
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.,Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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6
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Rykov SV, Filippova EA, Loginov VI, Braga EA. Gene Methylation in Circulating Cell-Free DNA from the Blood Plasma as Prognostic and Predictive Factor in Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Seale KN, Tkaczuk KHR. Circulating Biomarkers in Breast Cancer. Clin Breast Cancer 2021; 22:e319-e331. [PMID: 34756687 DOI: 10.1016/j.clbc.2021.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/22/2021] [Accepted: 09/19/2021] [Indexed: 12/11/2022]
Abstract
Breast cancer management has progressed immensely over the decades, but the disease is still a major source of morbidity and mortality worldwide. Even with enhanced imaging detection and tissue biopsy capabilities, disease can progress on an ineffective treatment before additional information is obtained through standard methods of response evaluation, including the RECIST 1.1 criteria, widely used for assessment of treatment response and benefit from therapy.6 Circulating biomarkers have the potential to provide valuable insight into disease progression and response to therapy, and they can serve to identify actionable mutations and tumor characteristics that can direct therapy. These biomarkers can be collected at higher frequencies than imaging or tissue sampling, potentially allowing for more informed management. This review will evaluate the roles of circulating biomarkers in breast cancer, including the serum markers Carcinoembryonic antigen CA15-3, CA27-29, HER2 ECD, and investigatory markers such as GP88; and the components of the liquid biopsy, including circulating tumor cells, cell free DNA/DNA methylation, circulating tumor DNA, and circulating microRNA.
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Affiliation(s)
- Katelyn N Seale
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201
| | - Katherine H R Tkaczuk
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201.
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8
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Tay TKY, Tan PH. Liquid Biopsy in Breast Cancer: A Focused Review. Arch Pathol Lab Med 2021; 145:678-686. [PMID: 32045277 DOI: 10.5858/arpa.2019-0559-ra] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 01/27/2023]
Abstract
CONTEXT.— The role of liquid biopsy in cancer management has been gaining increased prominence in the past decade, with well-defined clinical applications now being established in lung cancer. Recently, the US Food and Drug Administration also approved the Therascreen PIK3CA RGQ polymerase chain reaction assay as a companion diagnostic assay to detect PIK3CA mutations in breast cancer for both tissue and liquid biopsies, bringing the role of liquid biopsy in breast cancer management to the fore. Its utility in other aspects of breast cancer, however, is yet to be clearly defined. OBJECTIVE.— To review the studies that looked at liquid biopsies in breast cancer and examine their potential for clinical application in the areas of early diagnosis, prognostication, monitoring disease response, detecting minimal residual disease, and predicting risk of progression or relapse. We focus mainly on circulating tumor cells and circulating tumor DNA. DATA SOURCES.— Peer-reviewed articles in PubMed. CONCLUSIONS.— Liquid biopsies in breast cancers have yielded promising results, especially in the areas of monitoring treatment response and predicting disease progression or relapse. With further study, and hopefully coupled with continued improvements in technologies that isolate tumor-derived materials, liquid biopsies may go on to play a greater role in the breast cancer clinic.
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Affiliation(s)
- Timothy Kwang Yong Tay
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore
| | - Puay Hoon Tan
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore.,The Division of Pathology (Tan), Singapore General Hospital, Singapore
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9
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Zhu A, Yuan P, Hu N, Li M, Wang W, Wang X, Yue J, Wang J, Luo Y, Ma F, Zhang P, Li Q, Xu B, Cao S, Lippi G, Naito Y, Osman MA, Marta GN, Franceschini G, Orlandi A. Phase II study of apatinib in combination with oral vinorelbine in heavily pretreated HER2-negative metastatic breast cancer and clinical implications of monitoring ctDNA. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0418. [PMID: 34037346 PMCID: PMC8330536 DOI: 10.20892/j.issn.2095-3941.2020.0418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Apatinib is an oral TKI targeting VEGFR-2. Single-agent apatinib treatment has been shown to produce an objective response in patients with pretreated mBC. Oral vinorelbine also holds promise as a treatment of choice in patients with mBC. This study aimed to investigate the efficacy and safety of the oral vinorelbine-apatinib combination in patients with pretreated mBC. In addition, we detected gene variants in ctDNA to explore the therapeutic implications. METHODS This study enrolled patients with HER2-negative mBC who were pretreated with anthracycline/taxanes. Patients were treated with apatinib at 500 mg/425 mg daily plus oral vinorelbine 60 mg/m2 on days 1, 8, and 15 of every cycle (3 weeks). The primary endpoint was PFS. The secondary endpoints were ORR, CBR, OS, and safety. Patients eligible for ctDNA detection were evaluated before and during treatment. RESULTS Forty patients were enrolled. The median PFS was 5.2 months (95% CI, 3.4-7.0 months), and the median OS was 17.4 months (95% CI, 8.0-27.0 months). The ORR was 17.1% (6/35), and the CBR was 45.7% (16/35). The most common AEs included gastrointestinal reaction, myelosuppression, and hypertension. In 20 patients, ctDNA was detected at baseline and during treatment. A significant difference was found in PFS for undetected vs. detected baseline ctDNA (13.9 months vs. 3.6 months, P = 0.018). CONCLUSIONS All-oral therapy with apatinib plus vinorelbine displayed objective efficacy in patients with heavily pretreated HER2-negative mBC, with acceptable and manageable toxicity profiles. Patients with no gene variant detected and lower variant allele frequencies in ctDNA at baseline showed longer PFS.
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Affiliation(s)
- Anjie Zhu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Nanlin Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Mingzhou Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wenmiao Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Pin Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qing Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shanbo Cao
- AcornMed Biotechnology Co., Ltd., Beijing 101102, China
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University Hospital of Verona, Verona 37100, Italy
| | - Yoichi Naito
- Department of Breast and Medical Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Mohammed A. Osman
- Clinical Oncology, General Organization for Teaching Hospitals, Cairo 11435, Egypt
| | - Gustavo N. Marta
- Department of Radiation Oncology, Hospital Sírio-Libanês, Sao Paulo 01308-050, Brazil
| | - Gianluca Franceschini
- Multidisciplinary Breast Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome 00176, Italy
| | - Armando Orlandi
- Unit of Medical Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma 00176, Italy
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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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11
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Banys-Paluchowski M, Krawczyk N, Fehm T. Liquid Biopsy in Breast Cancer. Geburtshilfe Frauenheilkd 2020; 80:1093-1104. [PMID: 33173237 PMCID: PMC7647718 DOI: 10.1055/a-1124-7225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/02/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the blood-based analysis of circulating tumour cells (CTCs) and nucleic acids (DNA/RNA), otherwise known as liquid biopsy, has become increasingly important in breast cancer. Numerous trials have already underscored the high prognostic significance of CTC detection in both early and metastatic stages. Moreover, the changes in CTC levels and circulating tumour DNA (ctDNA) during the course of the disease correlate with the response to treatment. Research currently focuses on liquid-biopsy based therapeutic interventions in metastatic breast cancer. In this context, alpelisib, a PI3K inhibitor, was the first agent to be approved by FDA and EMA.
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Affiliation(s)
| | - Natalia Krawczyk
- Universitäts-Frauenklinik, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Tanja Fehm
- Universitäts-Frauenklinik, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
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12
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Liu Y, Du Q, Sun D, Han R, Teng M, Chen S, You H, Dong Y. Clinical applications of circulating tumor DNA in monitoring breast cancer drug resistance. Future Oncol 2020; 16:2863-2878. [PMID: 32976028 DOI: 10.2217/fon-2019-0760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is one of the leading causes of cancer-related deaths in women worldwide. Unfortunately, treatments often fail because of the development of drug resistance, the underlying mechanisms of which remain unclear. Circulating tumor DNA (ctDNA) is free DNA released into the blood by necrosis, apoptosis or direct secretion by tumor cells. In contrast to repeated, highly invasive tumor biopsies, ctDNA reflects all molecular alterations of tumors dynamically and captures both spatial and temporal tumor heterogeneity. Highly sensitive technologies, including personalized digital PCR and deep sequencing, make it possible to monitor response to therapies, predict drug resistance and tailor treatment regimens by identifying the genomic alteration profile of ctDNA, thereby achieving precision medicine. This review focuses on the current status of ctDNA biology, the technologies used to detect ctDNA and the potential clinical applications of identifying drug resistance mechanisms by detecting tumor-specific genomic alterations in breast cancer.
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Affiliation(s)
- Yang Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Qian Du
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Dan Sun
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Ruiying Han
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Mengmeng Teng
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Siying Chen
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Haisheng You
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yalin Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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13
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Detection of ctDNA with Personalized Molecular Barcode NGS and Its Clinical Significance in Patients with Early Breast Cancer. Transl Oncol 2020; 13:100787. [PMID: 32473569 PMCID: PMC7260577 DOI: 10.1016/j.tranon.2020.100787] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023] Open
Abstract
We attempted to detect circulating tumor DNA (ctDNA), taking advantage of molecular barcode next-generation sequencing (MB-NGS), which can be more easily customized to detect a variety of mutations with a high sensitivity than PCR-based methods. Sequencing with a gene panel consisting of the 13 most frequently mutated genes in breast tumors from stage I or II patients revealed 95 somatic mutations in the 12 genes in 62% (62/100) of tumors. Then, plasma DNA from each patient (n = 62) before surgery was analyzed via MB-NGS customized to each somatic mutation, resulting in the detection of ctDNA in 16.1% (10/62) of patients. ctDNA was significantly associated with biologically aggressive phenotypes, including large tumor size (P = .004), positive lymph node (P = .009), high histological grade (P < .001), negative ER (P = .018), negative PR (P = .017), and positive HER2 (P = .046). Furthermore, distant disease-free survival was significantly worse in patients with ctDNA (n = 10) than those without ctDNA (n = 52) (P < .001). Our results demonstrate that MB-NGS personalized to each mutation can detect ctDNA with a high sensitivity in early breast cancer patients at diagnosis, and it seems to have a potential to serve as a clinically useful tumor marker for predicting their prognosis.
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de Ruijter TC, van der Heide F, Smits KM, Aarts MJ, van Engeland M, Heijnen VCG. Prognostic DNA methylation markers for hormone receptor breast cancer: a systematic review. Breast Cancer Res 2020; 22:13. [PMID: 32005275 PMCID: PMC6993426 DOI: 10.1186/s13058-020-1250-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In patients with hormone receptor-positive breast cancer, differentiating between patients with a low and a high risk of recurrence is an ongoing challenge. In current practice, prognostic clinical parameters are used for risk prediction. DNA methylation markers have been proven to be of additional prognostic value in several cancer types. Numerous prognostic DNA methylation markers for breast cancer have been published in the literature. However, to date, none of these markers are used in clinical practice. METHODS We conducted a systematic review of PubMed and EMBASE to assess the number and level of evidence of published DNA methylation markers for hormone receptor-positive breast cancer. To obtain an overview of the reporting quality of the included studies, all were scored according to the REMARK criteria that were established as reporting guidelines for prognostic biomarker studies. RESULTS A total of 74 studies were identified reporting on 87 different DNA methylation markers. Assessment of the REMARK criteria showed variation in reporting quality of the studies. Eighteen single markers and one marker panel were studied in multiple independent populations. Hypermethylation of the markers RASSF1, BRCA, PITX2, CDH1, RARB, PCDH10 and PGR, and the marker panel GSTP1, RASSF1 and RARB showed a statistically significant correlation with poor disease outcome that was confirmed in at least one other, independent study. CONCLUSION This systematic review provides an overview on published prognostic DNA methylation markers for hormone receptor-positive breast cancer and identifies eight markers that have been independently validated. Analysis of the reporting quality of included studies suggests that future research on this topic would benefit from standardised reporting guidelines.
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Affiliation(s)
- Tim C. de Ruijter
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Frank van der Heide
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M. Smits
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Maureen J. Aarts
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Manon van Engeland
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C. G. Heijnen
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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Abstract
In only few years, circulating tumor DNA (ctDNA) in breast cancer has moved from purely fundamental research to nearby daily use for treatment selection and drug-resistance assessment. Indeed, technical advances and widespread use of next-generation sequencing or digital PCR allowed for detection of very low amount of tumor DNA in bloodstream. The use of ctDNA as liquid biopsy able either to monitor tumor burden under treatment or to overcome tumor heterogeneity and identify potential targetable drivers. Time has come to define how ctDNA can be implemented for early or metastatic breast cancer management. Data from retrospective analyses of prospective trials have recently highlighted the potential advantages but also the limitations of ctDNA, in particular for patients under endocrine therapy.
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen Cedex 1, France.
- Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France.
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Abe M, Kagara N, Miyake T, Tanei T, Naoi Y, Shimoda M, Shimazu K, Kim SJ, Noguchi S. Highly sensitive detection of sentinel lymph node metastasis of breast cancer by digital PCR for RASSF1A methylation. Oncol Rep 2019; 42:2382-2389. [PMID: 31638213 PMCID: PMC6826319 DOI: 10.3892/or.2019.7363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022] Open
Abstract
One-step nucleic acid amplification (OSNA) targeting cytokeratin 19 (CK19) mRNA expression and pathological examination are widely used for the intraoperative diagnosis of sentinel node (SN) metastasis. The aim of the present study was to develop a novel assay for detecting SN metastasis by targeting Ras association domain-containing protein 1 (RASSF1A) methylation in tumor cells, and to compare its performance with OSNA. Using digital PCR with methylation-specific restriction enzymes (RE-dMSP), our assay was able to detect ≥3 copies of methylated DNA per well, and was ≥10 times more sensitive than real-time PCR with bisulfite modification. OSNA lysates were examined using RE-dMSP and digital PCR for PIK3CA mutation, in the event that primary tumors were PIK3CA mutation-positive. RE-dMSP revealed a high concordance of 95.0% (153/161) with OSNA, and 100% (59/59) with PIK3CA mutation for detecting SN metastasis. In 11 breast cancer cell lines, the variation in methylated RASSF1A copy number was significantly lower than that of CK19 mRNA (2.8 vs. 10.5-fold; P<0.01). RE-dMSP has the potential to more accurately detect SN metastasis, and to more precisely estimate total tumor loads in SN, compared with OSNA.
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Affiliation(s)
- Mizuho Abe
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565‑0871, Japan
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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Role of Liquid Biopsy in Clinical Decision-Making for Breast Cancer. CURRENT BREAST CANCER REPORTS 2019. [DOI: 10.1007/s12609-019-0308-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gurioli G, Martignano F, Salvi S, Costantini M, Gunelli R, Casadio V. GSTP1 methylation in cancer: a liquid biopsy biomarker? Clin Chem Lab Med 2019; 56:702-717. [PMID: 29305565 DOI: 10.1515/cclm-2017-0703] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/31/2017] [Indexed: 12/14/2022]
Abstract
The coding region of GSTP1 gene is preceded by a large CpG-rich region that is frequently affected by methylation. In many cancer types, GSTP1 is affected by hypermethylation and, as a consequence, it has a low expression. The aim of this review is to give an overview on GSTP1 methylation studies with a special focus on liquid biopsy, thus to summarize methods, results, sample types, different diseases, to have a complete information regarding this promising epigenetic biomarker. We used all the most valuable scientific search engines (PubMed, Medline, Scopus and Web of Science) searching the following keywords: GSTP1, methylation, cancer, urine, serum, plasma and blood. GSTP1 is a largely investigated tissue biomarker in several malignancies such as prostate, breast, lung and hepatocellular carcinoma with good performances especially for diagnostic purposes. As a liquid biopsy biomarker, it has been mainly investigated in prostate cancer (PCa) where it showed a high specificity but a low sensitivity; thus, it is recommended in combination with other biomarkers. Despite the large number of published papers and the promising results, GSTP1 has not yet entered the clinical practice even for PCa diagnosis. For this reason, further large and prospective studies are needed to validate this assay.
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Affiliation(s)
- Giorgia Gurioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Filippo Martignano
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Matteo Costantini
- Pathology Unit, Department of Medical Oncology, Morgagni Pierantoni Hospital, Forlì, Italy
| | - Roberta Gunelli
- Department of Urology, Morgagni Pierantoni Hospital, Forli, Italy
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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Buono G, Gerratana L, Bulfoni M, Provinciali N, Basile D, Giuliano M, Corvaja C, Arpino G, Del Mastro L, De Placido S, De Laurentiis M, Cristofanilli M, Puglisi F. Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? Cancer Treat Rev 2019; 73:73-83. [PMID: 30682661 DOI: 10.1016/j.ctrv.2019.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
Abstract
Precision Medicine is becoming the new paradigm in healthcare as it enables better resources allocation, treatment optimization with a potential side-effects reduction and consequent impact on quality of life and survival. This revolution is being catalyzed by liquid biopsy technologies, which provide prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue-biopsy. In particular, circulating tumor DNA (ctDNA) is gaining momentum as a clinically feasible option capable to capture both spatial and temporal tumor heterogeneity. Several techniques are currently available for ctDNA extraction and analysis, each with its preferential case scenarios and preanalytical implications which must be taken into consideration to effectively support clinical decision-making and to better highlight its clinical utility. Aim of this review is to summarize both analytical developments and clinical evidences to offer a comprehensive update on the deployment of ctDNA in breast cancer's (BC) characterization and treatment.
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Affiliation(s)
- Giuseppe Buono
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Italy; Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michela Bulfoni
- Department of Pathology, ASUIUD University Hospital, Udine, Italy
| | | | - Debora Basile
- Department of Medicine (DAME), University of Udine, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy; Lester and Sue Smith Breast Center at Baylor College of Medicine, Houston, TX, USA
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Italy
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lucia Del Mastro
- Department of Medical Oncology, IRCCS AOU San Martino-IST, National Cancer Institute, Genova, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, PN, Italy
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Abstract
Cell-free DNA can be evaluated for the epigenetic component. Epigenetic alterations consist of changes in gene functions that do not involve changes in DNA sequence. The mainly studied epigenetic alteration is DNA methylation occurring at CpG islands in the promoter regions for which several literature data showed clinical relevance. This chapter is an overview of the epigenetic alterations detected in cell-free DNA.
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de Ruijter TC, Smits KM, Aarts MJ, van Hellemond IEG, Van Neste L, de Vries B, Peer PGM, Veeck J, van Engeland M, Tjan-Heijnen VCG. The trans-DATA study: aims and design of a translational breast cancer prognostic marker identification study. Diagn Progn Res 2019; 3:20. [PMID: 31641693 PMCID: PMC6796450 DOI: 10.1186/s41512-019-0065-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/12/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The effect of extended adjuvant aromatase inhibition in hormone-positive breast cancer after sequential tamoxifen, aromatase inhibitor treatment of 5 years was recently investigated by the DATA study. This study found no statistically significant effect of prolonged aromatase therapy. However, subgroup analysis showed post hoc statistically significant benefits in certain sub-populations. The trans-DATA study is a translational sub-study aiming to identify DNA methylation markers prognostic of patient outcome. METHODS Patients from the DATA study are included in the trans-DATA study. Primary breast tumour tissue will be collected, subtyped and used for DNA isolation. A genome-wide DNA methylation discovery assay will be performed on 60 patients that had a distant recurrence and 60 patients that did not have a distant recurrence using the Infinium Methylation EPIC Bead Chip platform. Differentially methylated regions of interest will be selected based on Akaike's Information Criterion, Gene Ontology Analysis and correlation between methylation and expression levels. Selected candidate genes will subsequently be validated in the remaining patients using qMSP. DISCUSSION The trans-DATA study uses a cohort derived from a clinical randomised trial. This study was designed to avoid common pitfalls in marker discovery studies such as selection bias, confounding and lack of reproducibility. In addition to the usual clinical risk factors, the results of this study may identify predictors of high recurrence risk in hormone receptor-positive breast cancer patients treated with sequential tamoxifen and aromatase inhibitor therapy.
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Affiliation(s)
- Tim C. de Ruijter
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kim M. Smits
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Maureen J. Aarts
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Irene E. G. van Hellemond
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Leander Van Neste
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Bart de Vries
- Department of Pathology, Zuyderland Medical Centre, Heerlen, The Netherlands
| | - Petronella G. M. Peer
- 0000 0004 0444 9382grid.10417.33Biostatistics, Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jürgen Veeck
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Manon van Engeland
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eDepartment of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vivianne C. G. Tjan-Heijnen
- 0000 0004 0480 1382grid.412966.eDivision of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- 0000 0004 0480 1382grid.412966.eGROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Allouchery V, Augusto L, Clatot F. Place des CTC et de l’ADN circulant dans la prise en charge du cancer du sein. ONCOLOGIE 2019. [DOI: 10.3166/onco-2019-0035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Si la présence de cellules tumorales circulantes (CTC) et d’ADN tumoral circulant (ADNtc) est connue de longue date, seuls les progrès technologiques récents ont permis d’évaluer l’intérêt de cette approche dans le cancer du sein. La détection de CTC, tant pour les cancers du sein localisés que métastatiques, est un facteur de mauvais pronostic établi, mais qui ne permet pas de proposer de prise en charge spécifique. L’usage de l’ADNtc nécessite des validations prospectives, mais semble particulièrement prometteur pour la recherche demaladie résiduelle ou l’identification de clones tumoraux porteurs de mutations (PI3KCA,ESR1) permettant de prédire l’efficacité ou la résistance thérapeutique.
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Li D, Li P, Wu J, Yi J, Dou Y, Guo X, Yin Y, Wang D, Ma C, Qiu L. Methylation of NBPF1 as a novel marker for the detection of plasma cell-free DNA of breast cancer patients. Clin Chim Acta 2018; 484:81-86. [DOI: 10.1016/j.cca.2018.05.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
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Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) isolated from plasma or serum by noninvasive procedures can serve as a "liquid biopsy" and has potential as a biomarker for the tumor burden and survival prediction of breast cancer (BC). However, its prognostic value in patients with BC is currently under debate. The aim of this meta-analysis was to investigate the relationship between cfDNA and survival outcome. METHODS We systematically searched PubMed, Embase, and Science Citation Index electronic databases for studies about the prognostic utility of cfDNA in patients with BC. The clinical characteristics, relapse/disease-free survival (RFS/DFS), and overall survival (OS) data were extracted from the eligible studies. The hazard ratios (HR) and 95% confidence intervals (CI) were calculated and pooled with a fixed-effects model using the Stata12.0 software. Subgroup and sensitivity analyses were also performed. RESULTS This meta-analysis included a total of 10 eligible studies and 1127 patients with BC. The pooled HR with 95% CI showed strong associations between cfDNA and OS (HR = 2.41, 95% CI, 1.83-3.16) along with DFS/RFS (HR = 2.73, 95% CI, 2.04-3.67) in patients with BC. Although publication bias was found in the studies regarding RFS/DFS, further trim and fill analysis revealed that the adjusted HR would be 2.53 (95% CI, 1.83-3.51), which is close to the original HR. Subgroup analyses confirmed the role of cfDNA as a strong prognostic marker in patients with BC, regardless of cfDNA analysis, sampling time, sample source, detection method, tumor stage, sample size, or area. CONCLUSIONS Our meta-analysis indicates that cfDNA is a strong predictive and prognostic marker in patients with BC.
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Affiliation(s)
| | - Chang Chu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, People's Republic of China
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Chang Y, Tolani B, Nie X, Zhi X, Hu M, He B. Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring. Ther Clin Risk Manag 2017; 13:1363-1374. [PMID: 29066904 PMCID: PMC5644666 DOI: 10.2147/tcrm.s141991] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.
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Affiliation(s)
- Yi Chang
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Xiuhong Nie
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiuyi Zhi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Mu Hu
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Biao He
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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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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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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Matsui S, Kagara N, Mishima C, Naoi Y, Shimoda M, Shimomura A, Shimazu K, Kim SJ, Noguchi S. Methylation of the SEPT9_v2 promoter as a novel marker for the detection of circulating tumor DNA in breast cancer patients. Oncol Rep 2016; 36:2225-35. [PMID: 27499429 DOI: 10.3892/or.2016.5004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/25/2016] [Indexed: 01/11/2023] Open
Abstract
The aim of the present study was to evaluate the promoter methylation status of SEPT9_v2 in breast cancer and to detect this methylated gene in circulating tumor DNA (ctDNA) in plasma. Bisulfite sequencing was performed with a next generation sequencer. Methylation of the SEPT9_v2 promoter was found in 67% (8/12) of breast cancer cell lines and 53% (10/19) of breast tumor tissue, but not in normal breast tissue (0/19). A clear inverse correlation was observed between the expression of SEPT9_v2 mRNA and the methylation index (MI) both in cell lines and breast cancer tissues. The MI of SEPT9_v2 was significantly higher in non-basal subtype of breast cancer (13.0%, n=84) than in basal subtype (3.0%, n=23) (P<0.0001). Methylated SEPT9_v2 ctDNA in plasma was detected in 11% (9/82) of primary breast cancer patients and 52% (26/50) of metastatic breast cancer patients, but not in the healthy controls (0/51). These results indicate that SEPT9_v2 promoter hypermethylation, which silences the expression of SEPT9_v2 mRNA, is observed in a significant proportion of breast tumors, and that methylated SEPT9_v2 may serve as a novel tumor marker for breast cancer.
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Affiliation(s)
- Saki Matsui
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Chieko Mishima
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Atsushi Shimomura
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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Takahashi H, Kagara N, Tanei T, Naoi Y, Shimoda M, Shimomura A, Shimazu K, Kim SJ, Noguchi S. Correlation of Methylated Circulating Tumor DNA With Response to Neoadjuvant Chemotherapy in Breast Cancer Patients. Clin Breast Cancer 2016; 17:61-69.e3. [PMID: 27395416 DOI: 10.1016/j.clbc.2016.06.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/19/2016] [Accepted: 06/08/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is known to harbor tumor-specific genetic or epigenetic alterations. In the present study, the correlation of ctDNA with tumor response to neoadjuvant chemotherapy (NAC) was evaluated in primary breast cancer patients. PATIENTS AND METHODS Plasma samples were obtained from 87 primary breast cancer patients (stage II-III) before and after NAC, as well as 1 year after surgery. Methylated ctDNA (met-ctDNA) was determined by one-step methylation-specific PCR (OS-MSP) for the promoter region of RASSF1A. RESULTS The positivity (23.0%, 20/87) of met-ctDNA before NAC was significantly (P < .05) higher than that of carcinoembryonic antigen (CEA) (8.6%) and cancer-associated antigen (CA) 15-3 (7.4%). In the patients with positive met-ctDNA before NAC, met-ctDNA significantly decreased after NAC in those with disease that responded to therapy (P = .006), but not in patients whose disease did not respond to therapy. Met-ctDNA after NAC was found to be significantly (P = .008) correlated to the extent of residual tumor burden. Of the 7 patients who showed an increase in met-ctDNA at 1 year after surgery, 3 developed recurrence. CONCLUSION Met-ctDNA is a more sensitive marker than CEA and CA15-3, and it might be useful in monitoring the clinical tumor response to NAC. In addition, the potential use of met-ctDNA as a tumor marker for monitoring postoperative recurrence has been suggested.
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Affiliation(s)
- Hiroyo Takahashi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan.
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Shimomura
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
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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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Warton K, Mahon KL, Samimi G. Methylated circulating tumor DNA in blood: power in cancer prognosis and response. Endocr Relat Cancer 2016; 23:R157-71. [PMID: 26764421 PMCID: PMC4737995 DOI: 10.1530/erc-15-0369] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) in the plasma or serum of cancer patients provides an opportunity for non-invasive sampling of tumor DNA. This 'liquid biopsy' allows for interrogations of DNA such as quantity, chromosomal alterations, sequence mutations and epigenetic changes, and can be used to guide and improve treatment throughout the course of the disease. This tremendous potential for real-time 'tracking' in a cancer patient has led to substantial research efforts in the ctDNA field. ctDNA can be distinguished from non-tumor DNA by the presence of tumor-specific mutations and copy number variations, and also by aberrant DNA methylation, with both DNA sequence and methylation changes corresponding to those found in the tumor. Aberrant methylation of specific promoter regions can be a very consistent feature of cancer, in contrast to mutations, which typically occur at a wide range of sites. This consistency makes ctDNA methylation amenable to the design of widely applicable clinical assays. In this review, we examine ctDNA methylation in the context of monitoring disease status, treatment response and determining the prognosis of cancer patients.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Kate L Mahon
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Goli Samimi
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
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Terry MB, McDonald JA, Wu HC, Eng S, Santella RM. Epigenetic Biomarkers of Breast Cancer Risk: Across the Breast Cancer Prevention Continuum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:33-68. [PMID: 26987530 PMCID: PMC5305320 DOI: 10.1007/978-3-319-22909-6_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic biomarkers, such as DNA methylation, can increase cancer risk through altering gene expression. The Cancer Genome Atlas (TCGA) Network has demonstrated breast cancer-specific DNA methylation signatures. DNA methylation signatures measured at the time of diagnosis may prove important for treatment options and in predicting disease-free and overall survival (tertiary prevention). DNA methylation measurement in cell free DNA may also be useful in improving early detection by measuring tumor DNA released into the blood (secondary prevention). Most evidence evaluating the use of DNA methylation markers in tertiary and secondary prevention efforts for breast cancer comes from studies that are cross-sectional or retrospective with limited corresponding epidemiologic data, raising concerns about temporality. Few prospective studies exist that are large enough to address whether DNA methylation markers add to the prediction of tertiary and secondary outcomes over and beyond standard clinical measures. Determining the role of epigenetic biomarkers in primary prevention can help in identifying modifiable pathways for targeting interventions and reducing disease incidence. The potential is great for DNA methylation markers to improve cancer outcomes across the prevention continuum. Large, prospective epidemiological studies will provide essential evidence of the overall utility of adding these markers to primary prevention efforts, screening, and clinical care.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| | - Jasmine A McDonald
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hui Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sybil Eng
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
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Polivka J, Pesta M, Janku F. Testing for oncogenic molecular aberrations in cell-free DNA-based liquid biopsies in the clinic: are we there yet? Expert Rev Mol Diagn 2015; 15:1631-44. [PMID: 26559503 DOI: 10.1586/14737159.2015.1110021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
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Affiliation(s)
- Jiri Polivka
- a Department of Histology and Embryology and Biomedical Centre, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic.,b Department of Neurology , Faculty Hospital Plzen , Plzen , Czech Republic
| | - Martin Pesta
- c Department of Biology, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic
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Mishima C, Kagara N, Matsui S, Tanei T, Naoi Y, Shimoda M, Shimomura A, Shimazu K, Kim SJ, Noguchi S. Promoter methylation of TRIM9 as a marker for detection of circulating tumor DNA in breast cancer patients. SPRINGERPLUS 2015; 4:635. [PMID: 26543769 PMCID: PMC4627990 DOI: 10.1186/s40064-015-1423-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/05/2022]
Abstract
The aim of the present study was
to investigate the promoter methylation status of TRIM9 in breast cancer and to determine the presence of TRIM9-methylated circulating tumor DNA (ctDNA) in plasma. Bisulfite sequencing with a next generation sequencer showed TRIM9 promoter methylation in 92 % (11/12) of breast cancer cell lines (BCCs) and 68 % (13/19) of breast tumor tissues but not in any normal breast tissues (0/19). Methylation ratio of TRIM9 was significantly lower in basal type (9 %, n = 23) than luminal A (69 %, n = 29, P = 0.0003). Quantitative RT-PCR of BCCs disclosed an inverse correlation between TRIM9 mRNA expression and methylation ratio. TRIM9 methylated ctDNA in plasma was detected in 18 % (10/56) of metastatic breast cancer patients but not in any of 60 healthy controls. These results indicate that TRIM9 promoter hypermethylation, which suppresses TRIM9 mRNA expression, occurs in a significant proportion of breast tumors, and that TRIM9-methylated ctDNA thus may serve as a tumor marker for breast cancer.
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Affiliation(s)
- Chieko Mishima
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Saki Matsui
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Atsushi Shimomura
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
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36
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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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Oshiro C, Kagara N, Naoi Y, Shimoda M, Shimomura A, Maruyama N, Shimazu K, Kim SJ, Noguchi S. PIK3CA mutations in serum DNA are predictive of recurrence in primary breast cancer patients. Breast Cancer Res Treat 2015; 150:299-307. [PMID: 25736040 DOI: 10.1007/s10549-015-3322-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/23/2015] [Indexed: 01/06/2023]
Abstract
We attempted to develop a highly sensitive and specific method for the detection of circulating tumor DNA (ctDNA) using a digital PCR (dPCR) assay for PIK3CA mutations (i.e., H1047R, E545K, and E542K) in primary breast cancer patients. The sensitivity of the dPCR assay for the mutant alleles was examined using cell lines with PIK3CA mutations and proved to be 0.01 %. Serum samples were collected pre-operatively from 313 stage I-III breast cancer patients, of whom 110 were found to have PIK3CA mutant tumors. The serum samples from these patients with PIK3CA mutant tumors were subjected to the dPCR assay, and 25 (22.7 %) were found to be positive. No PIK3CA mutant ctDNA was detected in the serum samples of 50 healthy women and 30 breast cancer patients with PIK3CA non-mutant tumors. The patients with PIK3CA mutant ctDNA were dichotomized into mutant ctDNA-high (ctDNA(high)) and ctDNA-low (ctDNA(low)) groups based on the median. The ctDNA(high) patients exhibited significantly shorter recurrence-free survival (RFS; P = 0.0002) and overall survival rates (OS; P = 0.0048) compared to those exhibited by the combined ctDNA(low) patient and ctDNA-free patient group. Multivariate analysis revealed that ctDNA(high) status significantly predicted poor RFS and OS and did so independently of conventional histological parameters. These results suggest that dPCR is a highly sensitive and specific method for the detection of PIK3CA mutant ctDNA and that ctDNA(high) but not ctDNA(low) status is a significant and independent prognostic factor for primary breast cancer patients.
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Affiliation(s)
- Chiya Oshiro
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, 2-2-E10 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan
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Fujita N, Kagara N, Yamamoto N, Shimazu K, Shimomura A, Shimoda M, Maruyama N, Naoi Y, Morimoto K, Oda N, Kim SJ, Noguchi S. Methylated DNA and high total DNA levels in the serum of patients with breast cancer following neoadjuvant chemotherapy are predictive of a poor prognosis. Oncol Lett 2014; 8:397-403. [PMID: 24959284 PMCID: PMC4063626 DOI: 10.3892/ol.2014.2068] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/20/2014] [Indexed: 01/05/2023] Open
Abstract
In a previous study, we established a one-step methylation-specific polymerase chain reaction (OS-MSP) assay for the detection of methylated DNA (met-DNA) and total DNA levels in serum. For the present study, this OS-MSP assay was used for patients with breast cancer treated with neoadjuvant chemotherapy (NAC) in order to investigate the prognostic significance of met-DNA and total DNA levels. Following treatment with NAC and prior to surgery, serum samples obtained from 120 patients with stage II/III breast cancer were subjected to the OS-MSP assay for analysis of the glutathione S-transferase pi 1, Ras association (RalGDS/AF-6) domain family member 1 and retinoic acid receptor β2 genes. The detection of methylation in a minimum of one of these genes indicated a positive outcome of the assay. The total DNA content of the serum was also determined. Of the 120 stage II/III patients, seven (6%) were positive for met-DNA in serum and showed a significantly worse overall survival (OS) time compared with patients negative for met-DNA (n=113) (5-year OS, 43 vs. 85%; P=0.002). The patients with high total DNA levels in serum (n=40) also showed a significantly worse OS compared with those with low total DNA levels (n=80) (65 vs. 91%; P<0.001). The presence of met-DNA and high total DNA levels in the serum were found to be significant prognostic factors that are independent of a pathological complete response by multivariate analysis. Following NAC, met-DNA and high total DNA levels in the serum detected with the OS-MSP assay constitute novel prognostic factors for patients with breast cancer; this may be clinically useful for the prognosis prediction for patients who do not achieve a pathological complete response following NAC.
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Affiliation(s)
- Noriko Fujita
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Noriaki Yamamoto
- Central Research Laboratories, Sysmex Corporation, Kobe 651-2271, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Atsushi Shimomura
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Naomi Maruyama
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Koji Morimoto
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Naofumi Oda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Suita-shi, Osaka 565-0871, Japan
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Marzese DM, Hirose H, Hoon DSB. Diagnostic and prognostic value of circulating tumor-related DNA in cancer patients. Expert Rev Mol Diagn 2014; 13:827-44. [DOI: 10.1586/14737159.2013.845088] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer. J Cancer Res Clin Oncol 2013. [PMID: 23479212 DOI: 10.1007/s00432‐013‐1413‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification in cfDNA during neoadjuvant chemotherapy. PATIENTS AND METHODS The study included 50 patients from a prospective cohort analyzed during neoadjuvant chemotherapy. Fifty healthy women with no history of cancer served as control group and 15 patients with metastatic breast cancer were used to validate the assay. Total cfDNA and HER2 gene amplification were measured by quantitative real-time polymerase chain reaction. RESULTS Plasma HER2 gene copy number (p = 0.794), HER2 gene amplification (p = 0.127) and total cfDNA (p = 0.440) did not differ significantly from the levels in the control group. Eighteen patients (36 %) obtained pathological complete response (pCR). HER2 gene copy number before the operation was significantly higher than the baseline level (p < 0.0001), but there was no difference between patients with and without pCR (p = 0.569). Likewise, there was no difference in plasma HER2 gene amplification between tissue HER2-positive and -negative patients (p = 0.754). CONCLUSIONS The results indicate that neither total cfDNA nor HER2 gene copy number is elevated in primary breast cancer patients compared to healthy controls. The level of both parameters increased during neoadjuvant chemotherapy, but without any relation to treatment effect. There was no indication of plasma HER2 gene amplification in the HER2-positive patients in the neoadjuvant setting.
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Bechmann T, Andersen RF, Pallisgaard N, Madsen JS, Maae E, Jakobsen EH, Bak Jylling AM, Steffensen KD, Jakobsen A. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer. J Cancer Res Clin Oncol 2013; 139:995-1003. [PMID: 23479212 DOI: 10.1007/s00432-013-1413-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 12/14/2022]
Abstract
PURPOSE Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification in cfDNA during neoadjuvant chemotherapy. PATIENTS AND METHODS The study included 50 patients from a prospective cohort analyzed during neoadjuvant chemotherapy. Fifty healthy women with no history of cancer served as control group and 15 patients with metastatic breast cancer were used to validate the assay. Total cfDNA and HER2 gene amplification were measured by quantitative real-time polymerase chain reaction. RESULTS Plasma HER2 gene copy number (p = 0.794), HER2 gene amplification (p = 0.127) and total cfDNA (p = 0.440) did not differ significantly from the levels in the control group. Eighteen patients (36 %) obtained pathological complete response (pCR). HER2 gene copy number before the operation was significantly higher than the baseline level (p < 0.0001), but there was no difference between patients with and without pCR (p = 0.569). Likewise, there was no difference in plasma HER2 gene amplification between tissue HER2-positive and -negative patients (p = 0.754). CONCLUSIONS The results indicate that neither total cfDNA nor HER2 gene copy number is elevated in primary breast cancer patients compared to healthy controls. The level of both parameters increased during neoadjuvant chemotherapy, but without any relation to treatment effect. There was no indication of plasma HER2 gene amplification in the HER2-positive patients in the neoadjuvant setting.
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Affiliation(s)
- Troels Bechmann
- The Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
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42
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Abstract
During tumor development, tumor cells release their nucleic acids into the blood circulation. This process occurs by apoptotic and necrotic cell deaths along with active cell secretion, resulting in high levels of circulating DNA, mRNA, and microRNA in the blood of patients with breast cancer. As circulating cell-free tumor nucleic acids may reflect the characteristics of the primary tumor and even of micrometastatic cells, they may be excellent blood biomarkers for screening breast cancer. Assays that allow the repetitive monitoring of patients by using blood samples as liquid biopsy may be efficient in assessing cancer progression in patients whose tumor tissue is not available. This review evaluates the recent data on the potential use of circulating cell-free nucleic acids as biomarkers for breast cancer.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246 Hamburg, Germany
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