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Leitão TP, Corredeira P, Kucharczak S, Rodrigues M, Piairo P, Rodrigues C, Alves P, Cavaco AM, Miranda M, Antunes M, Ferreira J, Palma Reis J, Lopes T, Diéguez L, Costa L. Clinical Validation of a Size-Based Microfluidic Device for Circulating Tumor Cell Isolation and Analysis in Renal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24098404. [PMID: 37176111 PMCID: PMC10178884 DOI: 10.3390/ijms24098404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Renal cell carcinoma (RCC) presents as metastatic disease in one third of cases. Research on circulating tumor cells (CTCs) and liquid biopsies is improving the understanding of RCC biology and metastases formation. However, a standardized, sensitive, specific, and cost-effective CTC detection technique is lacking. The use of platforms solely relying on epithelial markers is inappropriate in RCC due to the frequent epithelial-mesenchymal transition that CTCs undergo. This study aimed to test and clinically validate RUBYchip™, a microfluidic label-free CTC detection platform, in RCC patients. The average CTC capture efficiency of the device was 74.9% in spiking experiments using three different RCC cell lines. Clinical validation was performed in a cohort of 18 patients, eight non-metastatic (M0), five metastatic treatment-naïve (M1TN), and five metastatic progressing-under-treatment (M1TP). An average CTC detection rate of 77.8% was found and the average (range) total CTC count was 6.4 (0-27), 101.8 (0-255), and 3.2 (0-10), and the average mesenchymal CTC count (both single and clustered cells) was zero, 97.6 (0-255), and 0.2 (0-1) for M0, M1TN, and M1TP, respectively. CTC clusters were detected in 25% and 60% of M0 and M1TN patients, respectively. These results show that RUBYchip™ is an effective CTC detection platform in RCC.
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Affiliation(s)
- Tito Palmela Leitão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Urology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Patrícia Corredeira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sandra Kucharczak
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgsons gate 1, 7491 Trondheim, Norway
| | - Margarida Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Biological Engineering Department, Instituto Superior Técnico, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Paulina Piairo
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal
- RUBYnanomed Lda, Praça Conde de Agrolongo 123, 4700-312 Braga, Portugal
| | - Carolina Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Patrícia Alves
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Martins Cavaco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Miguel Miranda
- Urology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marília Antunes
- CEAUL-Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - José Palma Reis
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Urology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tomé Lopes
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal
- RUBYnanomed Lda, Praça Conde de Agrolongo 123, 4700-312 Braga, Portugal
| | - Luís Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Oncology Division, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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2
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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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Lopes C, Piairo P, Chícharo A, Abalde-Cela S, Pires LR, Corredeira P, Alves P, Muinelo-Romay L, Costa L, Diéguez L. HER2 Expression in Circulating Tumour Cells Isolated from Metastatic Breast Cancer Patients Using a Size-Based Microfluidic Device. Cancers (Basel) 2021; 13:4446. [PMID: 34503260 PMCID: PMC8431641 DOI: 10.3390/cancers13174446] [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: 08/13/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
HER2 is a prognostic and predictive biomarker in breast cancer, normally assessed in tumour biopsy and used to guide treatment choices. Circulating tumour cells (CTCs) escape the primary tumour and enter the bloodstream, exhibiting great metastatic potential and representing a real-time snapshot of the tumour burden. Liquid biopsy offers the unique opportunity for low invasive sampling in cancer patients and holds the potential to provide valuable information for the clinical management of cancer patients. This study assesses the performance of the RUBYchip™, a microfluidic system for CTC capture based on cell size and deformability, and compares it with the only FDA-approved technology for CTC enumeration, CellSearch®. After optimising device performance, 30 whole blood samples from metastatic breast cancer patients were processed with both technologies. The expression of HER2 was assessed in isolated CTCs and compared to tissue biopsy. Results show that the RUBYchipTM was able to isolate CTCs with higher efficiency than CellSearch®, up to 10 times more, averaging all samples. An accurate evaluation of different CTC subpopulations, including HER2+ CTCs, was provided. Liquid biopsy through the use of the RUBYchipTM in the clinic can overcome the limitations of histological testing and evaluate HER2 status in patients in real-time, helping to tailor treatment during disease evolution.
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Affiliation(s)
- Cláudia Lopes
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal; (C.L.); (A.C.); (S.A.-C.)
| | - Paulina Piairo
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal; (C.L.); (A.C.); (S.A.-C.)
| | - Alexandre Chícharo
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal; (C.L.); (A.C.); (S.A.-C.)
| | - Sara Abalde-Cela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal; (C.L.); (A.C.); (S.A.-C.)
| | - Liliana R. Pires
- RUBYnanomed Lda, Praça Conde de Agrolongo 123, 4700-312 Braga, Portugal;
| | - Patrícia Corredeira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (P.C.); (P.A.); (L.C.)
| | - Patrícia Alves
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (P.C.); (P.A.); (L.C.)
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), Complejo Hospitalario de Santiago de Compostela, Trav. Choupana s/n, 15706 Santiago de Compostela, Spain;
- CIBERONC, Centro de Investigación Biomédica en Red Cáncer, Calle de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Luís Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (P.C.); (P.A.); (L.C.)
- Oncology Division, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal; (C.L.); (A.C.); (S.A.-C.)
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Mabwa D, Gajjar K, Furniss D, Schiemer R, Crane R, Fallaize C, Martin-Hirsch PL, Martin FL, Kypraios T, Seddon AB, Phang S. Mid-infrared spectral classification of endometrial cancer compared to benign controls in serum or plasma samples. Analyst 2021; 146:5631-5642. [PMID: 34378554 DOI: 10.1039/d1an00833a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study demonstrates a discrimination of endometrial cancer versus (non-cancerous) benign controls based on mid-infrared (MIR) spectroscopy of dried plasma or serum liquid samples. A detailed evaluation was performed using four discriminant methods (LDA, QDA, kNN or SVM) to execute the classification task. The discriminant methods used in the study comprised methods that are widely used in the statistics (LDA and QDA) and machine learning literature (kNN and SVM). Of particular interest, is the impact of discrimination when presented with spectral data from a section of the bio-fingerprint region (1430 cm-1 to 900 cm-1) in contrast to the more extended bio-fingerprint region used here (1800 cm-1 to 900 cm-1). Quality metrics used were the misclassification rate, sensitivity, specificity, and Matthew's correlation coefficient (MCC). For plasma (with spectral data ranging from 1430 cm-1 to 900 cm-1), the best performing classifier was kNN, which achieved a sensitivity, specificity and MCC of 0.865 ± 0.043, 0.865 ± 0.023 and 0.762 ± 0.034, respectively. For serum (in the same wavenumber range), the best performing classifier was LDA, achieving a sensitivity, specificity and MCC of 0.899 ± 0.023, 0.763 ± 0.048 and 0.664 ± 0.067, respectively. For plasma (with spectral data ranging from 1800 cm-1 to 900 cm-1), the best performing classifier was SVM, with a sensitivity, specificity and MCC of 0.993 ± 0.010, 0.815 ± 0.000 and 0.815 ± 0.010, respectively. For serum (in the same wavenumber range), QDA performed best achieving a sensitivity, specificity and MCC of 0.852 ± 0.023, 0.700 ± 0.162 and 0.557 ± 0.012, respectively. Our findings demonstrate that even when a section of the bio-fingerprint region has been removed, good classification of endometrial cancer versus non-cancerous controls is still maintained. These findings suggest the potential of a MIR screening tool for endometrial cancer screening.
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Affiliation(s)
- David Mabwa
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Ketankumar Gajjar
- Obstetrics and Gynaecology, Nottingham University Hospitals NHS Trust - City Campus, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - David Furniss
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Roberta Schiemer
- Obstetrics and Gynaecology, Nottingham University Hospitals NHS Trust - City Campus, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Richard Crane
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Christopher Fallaize
- School of Mathematical Sciences, The Mathematical Sciences Building, University Park, University of Nottingham, NG7 2RD, UK
| | | | | | - Theordore Kypraios
- School of Mathematical Sciences, The Mathematical Sciences Building, University Park, University of Nottingham, NG7 2RD, UK
| | - Angela B Seddon
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Sendy Phang
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
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Wang YF, Wang XJ, Lu Z, Liu SR, Jiang Y, Wan XQ, Cheng CC, Shi LH, Wang LH, Ding Y. Overexpression of Stat3 increases circulating cfDNA in breast cancer. Breast Cancer Res Treat 2021; 187:69-80. [PMID: 33630196 DOI: 10.1007/s10549-021-06142-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Current studies on circulating cell-free DNA (cfDNA) have been focusing on its potential as biomarkers in liquid biopsy by detecting its content or genetic and epigenetic changes for the evaluation of tumor burden and therapeutic efficacy. However, the regulatory mechanism of cfDNA release remains unclear. Stat3 has been documented as an oncogene for the development and metastasis of breast cancer cells. In this study, we investigated whether Stat3 affects the release of cfDNA into blood and its association with the number of circulating tumor cells (CTCs). METHODS The cfDNA level in plasma of patients with breast cancer and healthy volunteers were determined by quantitative real-time PCR. Three mouse breast cancer models with different Stat3 expression were generated and used to established three breast cancer orthotopic animal models to examine the effect of Stat3 on cfDNA release in vivo. Stat3 mediated Epithelial-mesenchymal phenotype transition of CTCs was determined by immunofluorescence assay and Western blot assay. RESULTS The data showed that Stat3 increased circulating cfDNA, which is correlated with the increased volume of primary tumors and number of CTCs, accompanied with the dynamic EMT changes regulated by Snail induction. Furthermore, the high level of total circulating cfDNA and Stat3-cfDNA in patients with breast cancer were detected by quantitative real-time PCR using GAPDH and Stat3 primers. CONCLUSION Our results suggested that Stat3 increases the circulating cfDNA and CTCs in breast cancer.
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Affiliation(s)
- Yi-Fei Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xue-Jian Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Zhong Lu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Shu-Rong Liu
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yu Jiang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiao-Qing Wan
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Cong-Cong Cheng
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hong Shi
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Li-Hua Wang
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China.,Affiliated Hospital, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Yi Ding
- Laboratory of Molecular Oncology, Weifang Medical College, Weifang, 261053, Shandong, China. .,Key Laboratory of Applied Pharmacology, Weifang Medical University, Weifang, 261053, Shandong, China.
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Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
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Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:cells9030624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients’ stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a “PanCancer” detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
- Correspondence: or ; Tel.: +351-225084000; Fax: + 351-225084047
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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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9
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Salta S, P Nunes S, Fontes-Sousa M, Lopes P, Freitas M, Caldas M, Antunes L, Castro F, Antunes P, Palma de Sousa S, Henrique R, Jerónimo C. A DNA Methylation-Based Test for Breast Cancer Detection in Circulating Cell-Free DNA. J Clin Med 2018; 7:E420. [PMID: 30405052 PMCID: PMC6262630 DOI: 10.3390/jcm7110420] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Breast cancer (BrC) is the most frequent neoplasm in women. New biomarkers, including aberrant DNA methylation, may improve BrC management. Herein, we evaluated the detection and prognostic performance of seven genes' promoter methylation (APC, BRCA1, CCND2, FOXA1, PSAT1, RASSF1A and SCGB3A1). METHODS Methylation levels were assessed in primary BrC tissues by quantitative methylation-specific polymerase chain reaction (QMSP) and in circulating cell-free DNA (ccfDNA) by multiplex QMSP from two independent cohorts of patients (Cohort #1, n = 137; and Cohort #2, n = 44). Receiver operating characteristic (ROC) curves were constructed, and log-rank test and Cox regression were performed to assess the prognostic value of genes' methylation levels. RESULTS The gene-panel APC, FOXA1, RASSF1A, SCGB3A1 discriminated normal from cancerous tissue with high accuracy (95.55%). In multivariable analysis, high PSAT1-methylation levels [>percentile 75 (P75)] associated with longer disease-free survival, whereas higher FOXA1-methylation levels (>P75) associated with shorter disease-specific survival. The best performing panel in ccfDNA (APC, FOXA1 and RASSF1A) disclosed a sensitivity, specificity and accuracy over 70%. CONCLUSIONS This approach enables BrC accurate diagnosis and prognostic stratification in tissue samples, and allows for early detection in liquid biopsies, thus suggesting a putative value for patient management.
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Affiliation(s)
- Sofia Salta
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal.
| | - Sandra P Nunes
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal.
| | - Mário Fontes-Sousa
- Breast Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Paula Lopes
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Micaela Freitas
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
| | - Margarida Caldas
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Fernando Castro
- Breast Cancer Clinic and Department of Surgical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Pedro Antunes
- Breast Cancer Clinic and Department of Surgical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Susana Palma de Sousa
- Breast Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
| | - Rui Henrique
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), 4050-313 Porto, Portugal.
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10
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Lee JH, Jeong H, Choi JW, Oh HE, Kim YS. Liquid biopsy prediction of axillary lymph node metastasis, cancer recurrence, and patient survival in breast cancer: A meta-analysis. Medicine (Baltimore) 2018; 97:e12862. [PMID: 30334995 PMCID: PMC6211877 DOI: 10.1097/md.0000000000012862] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Liquid biopsies using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) have been developed for early cancer detection and patient monitoring. To investigate the clinical usefulness of ctDNA aberrations and cfDNA levels in patients with breast cancer (BC), we conducted a meta-analysis of 69 published studies on 5736 patients with BC. METHODS The relevant publications were identified by searching PubMed and Embase databases. The effect sizes of outcome parameters were pooled using a random-effects model. RESULTS The ctDNA mutation rates of TP53, PIK3CA, and ESR1 were approximately 38%, 27%, and 32%, respectively. High levels of cfDNA were associated with BCs rather than with healthy controls. However, these detection rates were not satisfactory for BC screening. Although the precise mechanisms have been unknown, high cfDNA levels were significantly associated with axillary lymph node metastasis (odds ratio [OR] = 2.148, P = .030). The ctDNA mutations were significantly associated with cancer recurrence (OR = 3.793, P < .001), short disease-free survival (univariate hazard ratio [HR] = 5.180, P = .026; multivariate HR = 3.605, P = .001), and progression-free survival (HR = 1.311, P = .013) rates, and poor overall survival outcomes (HR = 2.425, P = .007). CONCLUSION This meta-analysis demonstrates that ctDNA mutation status predicts disease recurrence and unfavorable survival outcomes, while cfDNA levels can be predictive of axillary lymph node metastasis in patients with BC.
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11
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Cao X, Tang Q, Holland-Letz T, Gündert M, Cuk K, Schott S, Heil J, Golatta M, Sohn C, Schneeweiss A, Burwinkel B. Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals. Int J Mol Sci 2018; 19:ijms19030900. [PMID: 29562656 PMCID: PMC5877761 DOI: 10.3390/ijms19030900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 01/26/2023] Open
Abstract
Breast cancer (BC) is the most common cancer among women and has high mortality rates. Early detection is supposed to be critical for the patient’s prognosis. In recent years, several studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop putative screening markers for cancer. However, most of the studies have not yet been validated. In our study, we analyzed the promoter methylation of RASSF1A and ATM in peripheral blood DNA of 229 sporadic patients and 151 healthy controls by the MassARRAY EpiTYPER assay. There were no significant differences in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. Furthermore, we performed the Infinium HumanMethylation450 BeadChip (450K) array analysis using 48 sporadic BC cases and 48 healthy controls (cases and controls are the same from those of the MassARRAY EpiTYPER assay) and made a comparison with the published data. No significant differences were presented in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. So far, the evidence for powerful blood-based methylation markers is still limited and the identified markers need to be further validated.
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Affiliation(s)
- Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Tim Holland-Letz
- Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Melanie Gündert
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Katarina Cuk
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Christof Sohn
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- National Centre for Tumor Diseases, Heidelberg 69120, Germany.
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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12
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Aberrantly Methylated DNA as a Biomarker in Breast Cancer. Int J Biol Markers 2018; 28:141-50. [DOI: 10.5301/jbm.5000009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2013] [Indexed: 11/20/2022]
Abstract
Aberrant DNA hypermethylation at gene promoters is a frequent event in human breast cancer. Recent genome-wide studies have identified hundreds of genes that exhibit differential methylation between breast cancer cells and normal breast tissue. Due to the tumor-specific nature of DNA hypermethylation events, their use as tumor biomarkers is usually not hampered by analytical signals from normal cells, which is a general problem for existing protein tumor markers used for clinical assessment of breast cancer. There is accumulating evidence that DNA-methylation changes in breast cancer patients occur early during tumorigenesis. This may open up for effective screening, and analysis of blood or nipple aspirate may later help in diagnosing breast cancer. As a more detailed molecular characterization of different types of breast cancer becomes available, the ability to divide patients into subgroups based on DNA biomarkers may improve prognosis. Serial monitoring of DNA-methylation markers in blood during treatment may be useful, particularly when the cancer burden is below the detection level for standard imaging techniques. Overall, aberrant DNA methylation has a great potential as a versatile biomarker tool for screening, diagnosis, prognosis and monitoring of breast cancer. Standardization of methods and biomarker panels will be required to fully exploit this clinical potential.
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13
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He K, Zhang L, Long X. Quantitative assessment of the association between APC promoter methylation and breast cancer. Oncotarget 2018; 7:37920-37930. [PMID: 27191268 PMCID: PMC5122360 DOI: 10.18632/oncotarget.9354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/26/2016] [Indexed: 12/15/2022] Open
Abstract
Adenomatous polyposis coli (APC) is an important tumor suppressor gene in breast cancer. However, there were inconsistent conclusions in the association between APC promoter methylation and breast cancer. Hence, we conducted a meta-analysis to quantitatively assess the clinicopathological significance and diagnosis role of APC methylation in breast cancer. In total, 3172 samples from 29 studies were performed in this study. The odds ratio (OR) of APC methylation was 5.92 (95% CI = 3.16–11.07) in breast cancer cases compared to controls,. The APC promoter methylation was associated with cancer stage (OR = 0.47, 95% CI = 0.28–0.80, P = 0.006), lymph node metastases (OR = 0.55, 95% CI = 0.36–0.84, P = 0.005) and ER status (OR = 1.34, 95% CI = 1.03–1.73, P = 0.003) in breast cancer. Furthermore, the sensitivity and specificity for all included studies were 0.444 (95% CI: 0.321–0.575, P < 0.0001) and 0.976 (95% CI: 0.916–0.993, P < 0.0001), respectively. These results suggested that APC promoter methylation was associated with breast cancer risk, and it could be a valuable biomarker for diagnosis, treatment and prognosis of breast cancer.
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Affiliation(s)
- Keli He
- Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.,Department of Clinical Laboratory, The First People's Hospital of Changde City, Changde, 415003, China
| | - Li Zhang
- Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xinghua Long
- Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
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14
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Beddowes E, Sammut SJ, Gao M, Caldas C. Predicting treatment resistance and relapse through circulating DNA. Breast 2017; 34 Suppl 1:S31-S35. [PMID: 28694015 DOI: 10.1016/j.breast.2017.06.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The use of circulating DNA(ctDNA) to provide a non-invasive, personalised genomic snapshot of a patients' tumour has huge potential. Over the past five years this area of research has gained huge momentum. A number of studies in metastatic breast cancer have shown the potential of ctDNA to predict prognosis and treatment response using ctDNA. Further developments have included deeper sequencing using whole exome and shallow whole genome approaches which has the potential to identify new mutations and chromosomal copy number changes which appear upon resistance to treatment. In early breast cancer, recent work utilising personalised digital PCR probes has shown huge potential in predicting disease relapse and the detection of micrometastatic disease which could lead to improved treatment and outcome for these patients. Specific pathways of resistance can also be monitored and liquid biopsy approaches for the detection of ESR1 mutations have been used which could identify patients who have become resistant to particular endocrine therapies. The identification of PIK3CA mutations in plasma has also been shown to predict a higher response rate to specific PI3K inhibitors and could be used as a non-invasive screening tool prior to treatment. Further work on the detection of exosomal miRNA and hypermethylated DNA in plasma have shown promise in terms of specificity for early breast cancer detection and could be used to monitor treatment response. This review will focus on technological advances in the field, early detection of relapse and the detection of tumour-specific genomic alterations which could predict treatment response and resistance in patients with breast cancer.
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Affiliation(s)
- Emma Beddowes
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Stephen J Sammut
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Meiling Gao
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Carlos Caldas
- Department of Oncology, University of Cambridge, and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom.
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15
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Kowalik A, Kowalewska M, Góźdź S. Current approaches for avoiding the limitations of circulating tumor cells detection methods-implications for diagnosis and treatment of patients with solid tumors. Transl Res 2017; 185:58-84.e15. [PMID: 28506696 DOI: 10.1016/j.trsl.2017.04.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Abstract
Eight million people die of cancer each year and 90% of deaths are caused by systemic disease. Circulating tumor cells (CTCs) contribute to the formation of metastases and thus are the subject of extensive research and an abiding interest to biotechnology and pharmaceutical companies. Recent technological advances have resulted in greatly improved CTC detection, enumeration, expansion, and culture methods. However, despite the fact that nearly 150 years have passed since the first detection and description of CTCs in human blood and enormous technological progress that has taken place in this field, especially within the last decade, few CTC detection methods have been approved for routine clinical use. This reflects the substantial methodological problems related to the nature of these cells, their heterogeneity, and diverse metastatic potential. Here, we provide an overview of CTC phenotypes, including the plasticity of CTCs and the relevance of inflammation and cell fusion phenomena for CTC biology. We also review the literature on CTC detection methodology-its recent improvements, clinical significance, and efforts of its clinical application in cancer patients management. At present, CTC detection remains a challenging diagnostic approach as a result of numerous current methodological limitations. This is especially problematic during the early stages of the disease due to the small numbers of CTCs released into the blood of cancer patients. Nonetheless, the rapid development of novel techniques of CTC detection and enumeration in peripheral blood is expected to expedite their implementation in the clinical setting. It is of utmost importance to understand the biology of CTCs and their distinct populations as a prerequisite for achieving this ultimate goal.
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Affiliation(s)
- Artur Kowalik
- Department of Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland; Department of Surgery and Surgical Nursing with the Scientific Research Laboratory, The Faculty of Health Sciences of the Jan Kochanowski University in Kielce, Kielce, Poland.
| | - Magdalena Kowalewska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warszawa, Poland; Department of Immunology, Biochemistry and Nutrition, Medical University of Warsaw, Warszawa, Poland
| | - Stanisław Góźdź
- Department of Clinical Oncology, Hollycross Cancer Center, Kielce, Poland; Department of Prevention and Cancer Epidemiology, Faculty of Health Sciences of the Jan Kochanowski University in Kielce, Kielce, Poland
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16
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Visvanathan K, Fackler MS, Zhang Z, Lopez-Bujanda ZA, Jeter SC, Sokoll LJ, Garrett-Mayer E, Cope LM, Umbricht CB, Euhus DM, Forero A, Storniolo AM, Nanda R, Lin NU, Carey LA, Ingle JN, Sukumar S, Wolff AC. Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC 005 Prospective Biomarker Study. J Clin Oncol 2016; 35:751-758. [PMID: 27870562 DOI: 10.1200/jco.2015.66.2080] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Purpose Epigenetic alterations measured in blood may help guide breast cancer treatment. The multisite prospective study TBCRC 005 was conducted to examine the ability of a novel panel of cell-free DNA methylation markers to predict survival outcomes in metastatic breast cancer (MBC) using a new quantitative multiplex assay (cMethDNA). Patients and Methods Ten genes were tested in duplicate serum samples from 141 women at baseline, at week 4, and at first restaging. A cumulative methylation index (CMI) was generated on the basis of six of the 10 genes tested. Methylation cut points were selected to maximize the log-rank statistic, and cross-validation was used to obtain unbiased point estimates. Logistic regression or Cox proportional hazard models were used to test associations between the CMI and progression-free survival (PFS), overall survival (OS), and disease status at first restaging. The added value of the CMI in predicting survival outcomes was evaluated and compared with circulating tumor cells (CellSearch). Results Median PFS and OS were significantly shorter in women with a high CMI (PFS, 2.1 months; OS, 12.3 months) versus a low CMI (PFS, 5.8 months; OS, 21.7 months). In multivariable models, among women with MBC, a high versus low CMI at week 4 was independently associated with worse PFS (hazard ratio, 1.79; 95% CI, 1.23 to 2.60; P = .002) and OS (hazard ratio, 1.75; 95% CI, 1.21 to 2.54; P = .003). An increase in the CMI from baseline to week 4 was associated with worse PFS ( P < .001) and progressive disease at first restaging ( P < .001). Week 4 CMI was a strong predictor of PFS, even in the presence of circulating tumor cells ( P = .004). Conclusion Methylation of this gene panel is a strong predictor of survival outcomes in MBC and may have clinical usefulness in risk stratification and disease monitoring.
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Affiliation(s)
- Kala Visvanathan
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - MaryJo S Fackler
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Zhe Zhang
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Zoila A Lopez-Bujanda
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Stacie C Jeter
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Lori J Sokoll
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Elizabeth Garrett-Mayer
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Leslie M Cope
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Christopher B Umbricht
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - David M Euhus
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Andres Forero
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Anna M Storniolo
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Rita Nanda
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Nancy U Lin
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Lisa A Carey
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - James N Ingle
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Saraswati Sukumar
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Antonio C Wolff
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
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Tang Q, Cheng J, Cao X, Surowy H, Burwinkel B. Blood-based DNA methylation as biomarker for breast cancer: a systematic review. Clin Epigenetics 2016; 8:115. [PMID: 27895805 PMCID: PMC5109688 DOI: 10.1186/s13148-016-0282-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently. Overall, 45 publications met the inclusion criteria for this review. DNA from whole blood, as well as cell-free DNA (cfDNA) from serum or plasma, was used in these studies. The most common method used for measuring global DNA methylation was the investigation of repetitive elements as surrogates and the application of array-based genome-wide methylation analysis. For measuring gene-specific methylation level, methylation-specific PCR and pyrosequencing were the most frequently used methods. Epigenome-wide blood DNA hypomethylation in BC patients were reported in several studies; however, the evidence is still not conclusive. The most frequently investigated gene in whole blood was BRCA1, which was found more frequently methylated in patients compared to controls. RASSF1A was the most widely investigated gene in cfDNA of serum or plasma, which was also found more frequently methylated in patients compared to controls. Several of the eligible studies reported the associations of global hypomethylation and increased BC risk. Studies investigated associations between gene-specific methylation and BC risk, while got heterogeneous results. But two studies reported that hypermethylation of ATM gene was associated with increased BC risk, which suggest the potential use of this gene for BC risk stratification. Overall, our review suggests the possibility of using blood-based DNA methylation marker as promising marker for BC risk stratification, as several studies found associations between certain methylation level in blood and BC risk. However, so far, the evidence is still quite limited. Optimal markers are yet to be developed and promising results needed to be validated in prospective study cohorts and tested in large screening populations.
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Affiliation(s)
- Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Cheng
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
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18
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Zhou D, Tang W, Wang W, Pan X, An HX, Zhang Y. Association between aberrant APC promoter methylation and breast cancer pathogenesis: a meta-analysis of 35 observational studies. PeerJ 2016; 4:e2203. [PMID: 27478702 PMCID: PMC4950556 DOI: 10.7717/peerj.2203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/10/2016] [Indexed: 12/01/2022] Open
Abstract
Background. Adenomatous polyposis coli (APC) is widely known as an antagonist of the Wnt signaling pathway via the inactivation of β-catenin. An increasing number of studies have reported that APC methylation contributes to the predisposition to breast cancer (BC). However, recent studies have yielded conflicting results. Methods. Herein, we systematically carried out a meta-analysis to assess the correlation between APC methylation and BC risk. Based on searches of the Cochrane Library, PubMed, Web of Science and Embase databases, the odds ratio (OR) with 95% confidence interval (CI) values were pooled and summarized. Results. A total of 31 articles involving 35 observational studies with 2,483 cases and 1,218 controls met the inclusion criteria. The results demonstrated that the frequency of APC methylation was significantly higher in BC cases than controls under a random effect model (OR = 8.92, 95% CI [5.12–15.52]). Subgroup analysis further confirmed the reliable results, regardless of the sample types detected, methylation detection methods applied and different regions included. Interestingly, our results also showed that the frequency of APC methylation was significantly lower in early-stage BC patients than late-stage ones (OR = 0.62, 95% CI [0.42–0.93]). Conclusion. APC methylation might play an indispensable role in the pathogenesis of BC and could be regarded as a potential biomarker for the diagnosis of BC.
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Affiliation(s)
- Dan Zhou
- Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Xiamen, China; Department of Translational Medicine, Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Fuzhou, China
| | - Weiwei Tang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University , Xiamen , China
| | - Wenyi Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University , Xiamen , China
| | - Xiaoyan Pan
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University , Xiamen , China
| | - Han-Xiang An
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University , Xiamen , China
| | - Yun Zhang
- Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Xiamen, China; Department of Translational Medicine, Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Fuzhou, China
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19
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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20
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Kristiansen S, Nielsen D, Sölétormos G. Detection and monitoring of hypermethylated RASSF1A in serum from patients with metastatic breast cancer. Clin Epigenetics 2016; 8:35. [PMID: 27042241 PMCID: PMC4818536 DOI: 10.1186/s13148-016-0199-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circulating hypermethylated RASSF1A could be a novel and potential useful marker for monitoring patients with metastatic breast cancer. Technical obstacles include fragmentation of the circulating DNA, fluctuations in the concentration, low concentrations of circulating tumor DNA, and different locations of methylation in the RASSF1A gene among patients. One common method for detection of hypermethylated genes is sodium bisulfite conversion of non-methylated cytosine to uracil, followed by detection with PCR. However, the method relies on full conversion of all non-methylated cytosines, cause strand breaks, and loss of DNA. Alternatively, methylation-sensitive restriction enzymes have been used to digest genomic DNA, as well as sodium bisulfite-treated DNA. By flanking different regions of the RASSF1A with different PCR primer pairs, we analyzed for methylated genomic regions resistant to cleavage by the methylation-sensitive restriction enzymes HpaII and BstUI. The goal was to find region(s) in RASSF1A with high sensitivity and specificity that could be used for monitoring. RESULTS The serum was spiked with non-human control DNA. By tracing the spiking control, the isolation procedure of the rare circulating tumor DNA was initially optimized. By analysis of production of PCR amplicons from HpaII- or BstUI-treated DNA isolated from 24 patients with metastatic breast cancer, we located four regions resulting in sensitivities from 63 to 83 %. When examining samples from 24 control subjects, these four regions gave a specificity of 100 %. Among these four regions, the primer pair with the highest PCR efficacy was selected to monitor the RASSF1A concentration in 31 collected serum samples. The spiked DNA was then used to calculate the tumor RASSF1A concentrations independent of fluctuations in circulating non-tumor DNA. As a proof of principle, there was concordance in the kinetics of the RASSF1A and the serological cancer biomarkers CA 15-3, CEA, and TPA. CONCLUSIONS Methylation-sensitive restriction enzymes may be a useful methodological approach for monitoring circulating hypermethylated RASSF1A among patients with metastatic breast cancer.
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Affiliation(s)
- Søren Kristiansen
- />Department of Clinical Biochemistry, Nordsjællands Hospital–Hillerød, University of Copenhagen, Dyrehavevej 29, DK-3400 Hillerød, Denmark
| | - Dorte Nielsen
- />Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark
| | - György Sölétormos
- />Department of Clinical Biochemistry, Nordsjællands Hospital–Hillerød, University of Copenhagen, Dyrehavevej 29, DK-3400 Hillerød, Denmark
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21
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Salvianti F, Orlando C, Massi D, De Giorgi V, Grazzini M, Pazzagli M, Pinzani P. Tumor-Related Methylated Cell-Free DNA and Circulating Tumor Cells in Melanoma. Front Mol Biosci 2016; 2:76. [PMID: 26779490 PMCID: PMC4705904 DOI: 10.3389/fmolb.2015.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 12/18/2022] Open
Abstract
Solid tumor release into the circulation cell-free DNA (cfDNA) and circulating tumor cells (CTCs) which represent promising biomarkers for cancer diagnosis. Circulating tumor DNA may be studied in plasma from cancer patients by detecting tumor specific alterations, such as genetic or epigenetic modifications. Ras association domain family 1 isoform A (RASSF1A) is a tumor suppressor gene silenced by promoter hypermethylation in a variety of human cancers including melanoma. The aim of the present study was to assess the diagnostic performance of a tumor-related methylated cfDNA marker in melanoma patients and to compare this parameter with the presence of CTCs. RASSF1A promoter methylation was quantified in cfDNA by qPCR in a consecutive series of 84 melanoma patients and 68 healthy controls. In a subset of 68 cases, the presence of CTCs was assessed by a filtration method (Isolation by Size of Epithelial Tumor Cells, ISET) as well as by an indirect method based on the detection of tyrosinase mRNA by RT-qPCR. The distribution of RASSF1A methylated cfDNA was investigated in cases and controls and the predictive capability of this parameter was assessed by means of the area under the ROC curve (AUC). The percentage of cases with methylated RASSF1A promoter in cfDNA was significantly higher in each class of melanoma patients (in situ, invasive and metastatic) than in healthy subjects (Pearson chi-squared test, p < 0.001). The concentration of RASSF1A methylated cfDNA in the subjects with a detectable quantity of methylated alleles was significantly higher in melanoma patients than in controls. The biomarker showed a good predictive capability (in terms of AUC) in discriminating between melanoma patients and healthy controls. This epigenetic marker associated to cfDNA did not show a significant correlation with the presence of CTCs, but, when the two parameters are jointly considered, we obtain a higher sensitivity of the detection of positive cases in invasive and metastatic melanomas. Our data suggest that cell-free tumor DNA and CTCs represent two complementary aspects of the liquid biopsy which may improve the diagnosis and the clinical management of melanoma patients.
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Affiliation(s)
- Francesca Salvianti
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Claudio Orlando
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Daniela Massi
- Division of Pathology, Department of Surgery and Translational Medicine, University of Florence Florence, Italy
| | - Vincenzo De Giorgi
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Marta Grazzini
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
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22
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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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23
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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24
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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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25
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Blood Tests for Colorectal Cancer Screening in the Standard Risk Population. CURRENT COLORECTAL CANCER REPORTS 2015. [DOI: 10.1007/s11888-015-0293-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Ito H, Hasegawa K, Hasegawa Y, Nishimaki T, Hosomichi K, Kimura S, Ohba M, Yao H, Onimaru M, Inoue I, Inoue H. Silver Nanoscale Hexagonal Column Chips for Detecting Cell-free DNA and Circulating Nucleosomes in Cancer Patients. Sci Rep 2015; 5:10455. [PMID: 25994878 PMCID: PMC4440038 DOI: 10.1038/srep10455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/13/2015] [Indexed: 01/05/2023] Open
Abstract
Blood tests, which are commonly used for cancer screening, generally have low sensitivity. Here, we developed a novel rapid and simple method to generate silver nanoscale hexagonal columns (NHCs) for use in surface-enhanced Raman scattering (SERS). We reported that the intensity of SERS spectra of clinical serum samples obtained from gastrointestinal cancer patients is was significantly higher than that of SERS spectra of clinical serum samples obtained from non-cancer patients. We estimated the combined constituents on silver NHCs by using a field emission-type scanning electron microscope, Raman microscopes, and a 3D laser scanning confocal microscope. We obtained the Raman scattering spectra of samples of physically fractured cells and clinical serum. No spectra were obtained for chemically lysed cultured cells and DNA, RNA, and protein extracted from cultured cells. We believe that our method, which uses SERS with silver NHCs to detect circulating nucleosomes bound by methylated cell-free DNA, may be successfully implemented in blood tests for cancer screening.
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Affiliation(s)
- Hiroaki Ito
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | | | | | - Tadashi Nishimaki
- Unit of Organ Oriented Medicine, Division of Digestive and General Surgery, Department of Medicine, Ryukyu University, Okinawa, Japan
| | | | - Satoshi Kimura
- Department of Laboratory Medicine and Central Clinical Laboratory, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Motoi Ohba
- Institute of Molecular Oncology, Showa University, Tokyo, Japan
| | - Hiroshi Yao
- Graduate School of Material Science, University of Hyogo, Hyogo, Japan
| | - Manabu Onimaru
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Haruhiro Inoue
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
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27
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Gao L, Xie E, Yu T, Chen D, Zhang L, Zhang B, Wang F, Xu J, Huang P, Liu X, Fang B, Pan S. Methylated APC and RASSF1A in multiple specimens contribute to the differential diagnosis of patients with undetermined solitary pulmonary nodules. J Thorac Dis 2015; 7:422-32. [PMID: 25922721 DOI: 10.3978/j.issn.2072-1439.2015.01.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/22/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Inactivation of tumor-suppressor gene (TSG) by promoter hypermethylation has been reported in many tumor types, including lung cancer. This study was designed to determine the methylated APC and RASSF1A genes in tumor tissue, serum and plasma of patients with early stage lung cancer. METHODS Eighty-nine patients with undetermined solitary pulmonary nodules detected upon CT-scan were recruited in this study. DNA samples were extracted from biopsy tissues, serum and plasma and QMSP of APC and RASSF1A was carried out after bisulfite conversion. The 89 patients consist of 58 stage I lung cancer patients and 31 benign lung disease according to pathological report. Twenty-six cancer patients had matched biopsy tumor tissue, serum and plasma samples. RESULTS The methylation rates of APC and RASSF1A were 59.0% and 66.1% in biopsy tissues, 42.5% and 52.5% in serum, and 24.1% and 43.1% in plasma of cancer patients. For RASSF1A, different samples all showed a significant difference between cancer group and benign group (P<0.05). However, APC gene only explored the P value less than 0.05 in plasma result. Towards the 26 lung cancer patients with three matched samples, methylation rate in each sample type was more than 50.0% and displayed no difference. CONCLUSIONS Evaluation of APC and RASSF1A promoter methylation by using QMSP appears to be very useful for the differential diagnosis of patients with undetermined solitary pulmonary nodules. Our results also suggested that plasma might be the best sample for clinical detection of early stage lung.
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Affiliation(s)
- Li Gao
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erfu Xie
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tongfu Yu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Chen
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lixia Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bingfeng Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fang Wang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Xu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peijun Huang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xisheng Liu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bingliang Fang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiyang Pan
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Fu D, Ren C, Tan H, Wei J, Zhu Y, He C, Shao W, Zhang J. Sox17 promoter methylation in plasma DNA is associated with poor survival and can be used as a prognostic factor in breast cancer. Medicine (Baltimore) 2015; 94:e637. [PMID: 25789956 PMCID: PMC4602484 DOI: 10.1097/md.0000000000000637] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aberrant DNA methylation that leads to the inactivation of tumor suppressor genes is known to play an important role in the development and progression of breast cancer. Methylation status of cancer-related genes is considered to be a promising biomarker for the early diagnosis and prognosis of tumors. This study investigated the methylation status of the Sox17 gene in breast cancer tissue and its corresponding plasma DNA to evaluate the association of methylation levels with clinicopathological parameters and prognosis.The methylation status of the Sox17 gene promoter was evaluated with methylation-specific polymerase chain reaction (MSP) in 155 paired breast cancer tissue and plasma samples and in 60 paired normal breast tissue and plasma samples. Association of Sox17 methylation status with clinicopathological parameters was analyzed by χ tests. Overall and disease-free survival (DFS) curves were calculated using Kaplan-Meier analysis, and the differences between curves were analyzed by log-rank tests.The frequency of Sox17 gene methylation was 72.9% (113/155) in breast cancer tissues and 58.1% (90/155) in plasma DNA. Sox17 gene methylation was not found in normal breast tissues or in their paired plasma DNA. There was a significant correlation of Sox17 methylation between corresponding tumor tissues and paired plasma DNA (r = 0.688, P < 0.001). Aberrant Sox17 methylation in cancer tissues and in plasma DNA was significantly associated with the tumor node metastasis stage (P = 0.035 and P = 0.001, respectively) and with lymph node metastasis (P < 0.001 and P = 0.001, respectively). Kaplan-Meier survival curves showed that aberrant Sox17 promoter methylation in cancer tissues and plasma DNA was associated with poor DFS (P < 0.005) and overall survival (OS) (P < 0.005). Multivariate analysis showed that Sox17 methylation in plasma DNA was an independent prognostic factor in breast cancer for both DFS (P = 0.020; hazard ratio [HR] = 2.142; 95% confidence interval [CI]: 1.128-4.067) and for OS (P = 0.001; HR = 4.737; 95% CI: 2.088-10.747).Sox17 gene promoter methylation may play an important role in breast cancer progression and could be used as a prognostic biomarker to identify patients at risk of developing metastasis or recurrence after mastectomy.
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Affiliation(s)
- Deyuan Fu
- From the Department of Thyroid and Breast Surgery (DF, HT, JW, YZ, CH, WS, JZ); and Clinical Medical Testing Laboratory (CR), Northern Jiangsu People's Hospital and Clinical Medical College of Yangzhou University, Yangzhou, China
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Bidard FC, Weigelt B, Reis-Filho JS. Going with the flow: from circulating tumor cells to DNA. Sci Transl Med 2014; 5:207ps14. [PMID: 24132635 DOI: 10.1126/scitranslmed.3006305] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular analyses of circulating tumor DNA (ctDNA) in plasma from cancer patients have the potential to deliver minimally invasive diagnostic and disease-monitoring biomarkers. Drawing from experience gained through the translation of circulating tumor cell detection to clinical tests, we discuss ctDNA as a source of tumor material for biomarker development.
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Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
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Rafii A, Touboul C, Al Thani H, Suhre K, Malek JA. Where cancer genomics should go next: a clinician's perspective. Hum Mol Genet 2014; 23:R69-75. [PMID: 24833724 DOI: 10.1093/hmg/ddu234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Large-scale, genomic studies of specific tumors such as The Cancer Genome Atlas have provided a better understanding of the alterations of pathways involved in the development of solid tumors including glioblastoma, breast cancer, ovarian and endometrial cancers, colon cancer and lung squamous cell carcinoma. This tremendous effort of the scientific community has confirmed the view that cancer actually represents a wide variety of diseases originating from different organs. These studies showed that TP53 and PI3KCA are the two most mutated genes in all types of cancers and that 30-70% of all solid tumors harbor potentially 'actionable' mutations that can be exploited for patient stratification or treatment optimization. Translation of this huge oncogenomic data set to clinical application in personalized medicine programs is now the main challenge for the future. The gap between our basic knowledge and clinical application is still wide. Closing the gap will require translational personalized trials, which may initiate a radical change in our routine clinical practice in oncology.
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Affiliation(s)
- A Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar, Department of Genetic Medicine, Weill Cornell Medical College, New York, USA, Faculté de Médecine de Montpellier, Department of Gynecologic Oncology, Hôpital Arnaud de Villeneuve, Montpellier, France,
| | - C Touboul
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar, Faculté de Médecine de Créteil UPEC-Paris XII. UMR INSERM U965 : Angiogenèse et Recherche Translationnelle, Hôpital Lariboisière, 49 bd de la Chapelle, 75010 Paris, France
| | - H Al Thani
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - K Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College-Qatar, Doha, Qatar and Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - J A Malek
- Department of Genetic Medicine, Weill Cornell Medical College, New York, USA
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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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Esposito A, Bardelli A, Criscitiello C, Colombo N, Gelao L, Fumagalli L, Minchella I, Locatelli M, Goldhirsch A, Curigliano G. Monitoring tumor-derived cell-free DNA in patients with solid tumors: clinical perspectives and research opportunities. Cancer Treat Rev 2013; 40:648-55. [PMID: 24184333 DOI: 10.1016/j.ctrv.2013.10.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/11/2013] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA represents a non-invasive biomarker, as it can be isolated from human plasma, serum and other body fluids. Circulating tumor DNA shed from primary and metastatic cancers may allow the non-invasive analysis of the evolution of tumor genomes during treatment and disease progression through 'liquid biopsies'. The serial monitoring of tumor genotypes, which are instable and prone to changes under selection pressure, is becoming increasingly possible. The "liquid biopsy" provide novel biological insights into the process of metastasis and may elucidate signaling pathways involved in cell invasiveness and metastatic competence. This review will focus on the clinical utility of circulating cell free DNA in main solid tumors, including genetic and epigenetic alterations that can be detected.
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Affiliation(s)
- Angela Esposito
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy; IRCC Institute for Cancer Research and Treatment, Candiolo, Torino, Italy; FIRC Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Carmen Criscitiello
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Nicoletta Colombo
- Division of Gynecologic Oncology, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Lucia Gelao
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Luca Fumagalli
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Ida Minchella
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Marzia Locatelli
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Aron Goldhirsch
- Breast Cancer Program Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, Istituto Europeo di Oncologia, Via Ripamonti 435, 20133 Milano, Italy.
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Abstract
Distant metastases harbor unique genomic characteristics not detectable in the corresponding primary tumor of the same patient and metastases located at different sites show a considerable intrapatient heterogeneity. Thus, the mere analysis of the resected primary tumor alone (current standard practice in oncology) or, if possible, even reevaluation of tumor characteristics based on the biopsy of the most accessible metastasis may not reveal sufficient information for treatment decisions. Here, we propose that this dilemma can be solved by a new diagnostic concept: liquid biopsy, that is, analysis of therapeutic targets and drug resistance-conferring gene mutations on circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA) released into the peripheral blood from metastatic deposits. We discuss the current challenges and future perspectives of CTCs and ctDNA as biomarkers in clinical oncology. Both CTCs and ctDNA are interesting complementary technologies that can be used in parallel in future trials assessing new drugs or drug combinations. We postulate that the liquid biopsy concept will contribute to a better understanding and clinical management of drug resistance in patients with cancer.
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Affiliation(s)
- Klaus Pantel
- Authors' Affiliations: Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; University Medical Centre, Saint-Eloi Hospital, Institute of Research in Biotherapy, Laboratory of Rare Human Circulating Cells, Cell and Tissue Biopathology of Tumors Department; and University Institute of Clinical Research UM1-EA2415-Epidemiology, Biostatistics & Public Health, Montpellier, France
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36
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Elshimali YI, Khaddour H, Sarkissyan M, Wu Y, Vadgama JV. The clinical utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients. Int J Mol Sci 2013; 14:18925-58. [PMID: 24065096 PMCID: PMC3794814 DOI: 10.3390/ijms140918925] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 02/06/2023] Open
Abstract
Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed.
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Affiliation(s)
- Yahya I. Elshimali
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +1-818-515-7618; Fax: +1-818-994-9875
| | - Husseina Khaddour
- Laboratory Diagnostic Medicine, Faculty of Pharmacy, Mazzeh (17th April Street), Damascus University, Damascus, Syria; E-Mail:
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
| | - Yanyuan Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
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Bidard FC, Madic J, Mariani P, Piperno-Neumann S, Rampanou A, Servois V, Cassoux N, Desjardins L, Milder M, Vaucher I, Pierga JY, Lebofsky R, Stern MH, Lantz O. Detection rate and prognostic value of circulating tumor cells and circulating tumor DNA in metastatic uveal melanoma. Int J Cancer 2013; 134:1207-13. [PMID: 23934701 DOI: 10.1002/ijc.28436] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/25/2013] [Indexed: 12/13/2022]
Abstract
Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been recently investigated in several cancer types, but their respective clinical significance remains to be determined. In our prospective study, we compared the detection rate and the prognostic value of these two circulating biomarkers in patients with metastatic uveal melanoma. GNAQ/GNA11 mutations were characterized in archived tumor tissue. Using a highly sensitive and mutation-specific bidirectional pyrophosphorolysis-activated polymerization (bi-PAP) technique, GNAQ c.626A>T, GNAQ c.626A>C and GNA11 c.626A>T copy numbers were quantified in plasma from 12 mL of blood. CTCs were detected at the same time in 7.5 mL of blood by the CellSearch technique. Patient characteristics and outcome were prospectively collected. CTCs (≥1) were detected in 12 of the 40 included patients (30%, range 1-20). Among the 26 patients with known detectable mutations, ctDNA was detected and quantified in 22 (84%, range 4-11,421 copies/mL). CTC count and ctDNA levels were associated with the presence of miliary hepatic metastasis (p = 0.004 and 0.03, respectively), with metastasis volume (p = 0.005 and 0.004) and with each other (p < 0.0001). CTC count and ctDNA levels were both strongly associated with progression-free survival (p = 0.003 and 0.001) and overall survival (p = 0.0009 and <0.0001). In multivariate analyses, ctDNA appeared to be a better prognostic marker than CTC. In conclusion, ctDNA and CTC are correlated and both have poor prognostic significance. CTC detection can be performed in every patient but, in patients with detectable mutations, ctDNA was more frequently detected than CTC and has possibly more prognostic value.
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Affiliation(s)
- François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris, France; Laboratory of Circulating Tumor Biomarkers, Institut Curie, Paris, France
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Guttery DS, Blighe K, Page K, Marchese SD, Hills A, Coombes RC, Stebbing J, Shaw JA. Hide and seek: tell-tale signs of breast cancer lurking in the blood. Cancer Metastasis Rev 2013; 32:289-302. [PMID: 23108389 DOI: 10.1007/s10555-012-9414-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Breast cancer treatment is improving due to the introduction of new drugs, guided by molecular testing of the primary tumour for mutations/oncogenic drivers (e.g. HER2 gene amplification). However, tumour tissue is not always available for molecular analysis, intra-tumoural heterogeneity is common and the "cancer genome" is known to evolve with time, particularly following treatment as resistance develops. After resection, those patients with only residual micrometastases are likely to be cured but those with radiologically detectable overt disease are not. Thus, the discovery of blood test(s) that could (1) alert clinicians to early primary or recurrent disease and (2) monitor response to treatment could impact significantly on mortality. Towards this, we and others have focused on molecular profiling of circulating nucleic acids isolated from plasma, both cell-free DNA (cfDNA) and microRNAs, and the relationship of these to circulating tumour cells (CTCs). This review considers the utility of each as circulating biomarkers in breast cancer with particular emphasis on the bioinformatic tools available to support molecular profiling.
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Affiliation(s)
- David S Guttery
- Department of Cancer Studies and Molecular Medicine, Leicester Royal Infirmary, Leicester, UK.
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Twelves D, Nerurkar A, Osin P, Dexter T, Ward A, Gui GPH, Isacke CM. DNA promoter hypermethylation profiles in breast duct fluid. Breast Cancer Res Treat 2013; 139:341-50. [PMID: 23674191 DOI: 10.1007/s10549-013-2544-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 04/19/2013] [Indexed: 12/31/2022]
Abstract
DNA methylation of tumor-suppressor genes occurs early in the molecular transformation of precursor events to breast cancer and is therefore of interest to screening in high-risk women. The aim of this study was to use tumor-suppressor genes that have previously been shown to be cancer predictive in tissue to evaluate the potential of DNA methylation assays in cells from duct lavage (DL) fluid. The frequency of target gene DNA methylation in tissue and DL of cancer and healthy control patients was assessed, and an association of DNA methylation between different duct systems in the same breast was explored. The cancer and control groups were identified in the outpatient clinic when surgical treatment was finalized. Tumor, adjacent tissue and bilateral DL samples for comparative DNA methylation studies were obtained during surgery from women with cancer. In the healthy control group, samples of tissue and DL were collected. Reverse transcriptase methylation-specific PCR was conducted on modified DNA purified from 42 cancer biopsies, 41 benign excision cavity biopsies (internal control), 29 benign biopsies (external control), and 119 DL specimens. A validated panel of cancer predictive genes was analyzed in the study bank of tissue and DL samples from cancer and healthy patients. The sensitivity of DNA methylation in DL samples compared with matched cancer tissue was highest for SCGB3A1 (90 %), CDH13 (91 %), and RARB (83 %). The genetic algorithm selected RASSF1A, RARB, and IGFBP7 as the optimum predictor set for detecting DNA methylation in cancer tissue. The optimum area under the ROC curve for DNA methylation in cancer compared with internal control healthy tissue from excision margins was 0.84. The area under the ROC curve for DNA methylation in cancer DL compared with contralateral benign DL was 0.76. DL cytology was not a helpful predictor of breast cancer. This study shows that relative patterns of tumor-suppressor gene hypermethylation in breast cancer tissue are significantly reflected in the DL from the cancer affected breast. Using DL, nonconcordant patterns of DNA methylation between different duct systems confer independent oncologic potential for distinct breast lobes. The approach of DNA methylation in DL may be substantiated by a larger trial of breast cancer biomarkers.
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Affiliation(s)
- Dominique Twelves
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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Moleres A, Campión J, Milagro FI, Marcos A, Campoy C, Garagorri JM, Gómez-Martínez S, Martínez JA, Azcona-Sanjulián MC, Martí A. Differential DNA methylation patterns between high and low responders to a weight loss intervention in overweight or obese adolescents: the EVASYON study. FASEB J 2013; 27:2504-12. [PMID: 23475851 DOI: 10.1096/fj.12-215566] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In recent years, epigenetic markers emerged as a new tool to understand the influence of lifestyle factors on obesity phenotypes. Adolescence is considered an important epigenetic window over a human's lifetime. The objective of this work was to explore baseline changes in DNA methylation that could be associated with a better weight loss response after a multidisciplinary intervention program in Spanish obese or overweight adolescents. Overweight or obese adolescents (n=107) undergoing 10 wk of a multidisciplinary intervention for weight loss were assigned as high or low responders to the treatment. A methylation microarray was performed to search for baseline epigenetic differences between the 2 groups (12 subjects/group), and MALDI-TOF mass spectrometry was used to validate (n=107) relevant CpG sites and surrounding regions. After validation, 5 regions located in or near AQP9, DUSP22, HIPK3, TNNT1, and TNNI3 genes showed differential methylation levels between high and low responders to the multidisciplinary weight loss intervention. Moreover, a calculated methylation score was significantly associated with changes in weight, BMI-SDS, and body fat mass loss after the treatment. In summary, we have identified 5 DNA regions that are differentially methylated depending on weight loss response. These methylation changes may help to better understand the weight loss response in obese adolescents.
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Affiliation(s)
- Adriana Moleres
- Department of Nutrition, Food Science, Physiology, and Toxicology, University of Navarra, Pamplona, Spain
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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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Methylated APC and GSTP1 genes in serum DNA correlate with the presence of circulating blood tumor cells and are associated with a more aggressive and advanced breast cancer disease. Eur J Med Res 2012; 15:277-86. [PMID: 20696638 PMCID: PMC3351951 DOI: 10.1186/2047-783x-15-7-277] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Tumor-related methylated DNA and circulating tumor cells (CTC) in the peripheral blood might be of prognostic importance in breast cancer. Thus, the aim of our study was to examine free methylated DNA and CTC in the blood from breast cancer patients and to correlate it with clinicopathological features known to influence prognosis. Materials and methods We prospectively obtained serum samples from 85 patients with breast cancer and 22 healthy volunteers. Sera were analysed by methylation specific PCR (MethyLight PCR) for five genes: adenomatous polyposis coli (APC), ras association domain family protein 1A (RASSF1A), estrogen receptor 1 (ESR1), CDKN2A (p16) and glutathione s-transferase pi 1 (GSTP1). Beta actin (ACTB) served as control. In parallel matched peripheral blood of 63 patients was used to assay for circulating tumor cells in the peripheral blood by a modified immunomagnetic AdnaTest BreastCancerSelect with PCR detection for EPCAM, MUC1, MGB1 and SPDEF. Results We found a hypermethylation in the APC gene in 29% (25/85), in RASSF1A in 26% (22/85), in GSTP1 in 18% (14/76) and in ESR1 in 38% (32/85) of all breast cancer patients. No hypermethylation of CDKN2A was found (0/25). Blood samples of patients were defined CTC positive by detecting the EPCAM 13% (8/63), MUC1 16% (10/63), MGB 9% (5/55), SPDEF 12% (7/58) and in 27% detecting one or more genes (15/55). A significant difference was seen in methylated APC DNA between cancer patients and healthy volunteers. Moreover, methylated APC, RASSF1 and CTC were significantly different in metastatic versus non-metastatic disease. In addition, the presence of methylated APC, RASSF1A and CTC correlated significantly with AJCC-staging (p = 0.001, p = 0.031 and 0.002, respectively). High incidences of methylations were found for the genes RASSF1 and ESR1 in healthy individuals (both 23% 5/22). Methylated GSTP1 was predominantly found in the serum of patients with large primaries (p = 0.023) and was highly significantly correlated with positive Her2/neu status (p = 0.003). Elevated serum CA15.3 was strongly correlated with methylated APC and CTC detection (both p = 0.000). Methylated ESR1 failed to exhibit significant correlations with any of the above mentioned parameters. The presence of CTC in peripheral blood was significantly associated with methylated APC (p = 0.012) and methylated GSTP1 (p = 0.001). Conclusion The detection of methylated APC and GSTP1 DNA in serum correlated with the presence of CTC in the blood of breast cancer patients. Both methylated DNA and CTC correlated with a more aggressive tumor biology and advanced disease.
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Fujita N, Nakayama T, Yamamoto N, Kim SJ, Shimazu K, Shimomura A, Maruyama N, Morimoto K, Tamaki Y, Noguchi S. Methylated DNA and total DNA in serum detected by one-step methylation-specific PCR is predictive of poor prognosis for breast cancer patients. Oncology 2012; 83:273-82. [PMID: 22964822 DOI: 10.1159/000342083] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/13/2012] [Indexed: 01/05/2023]
Abstract
PURPOSE We recently developed the one-step methylation-specific PCR (OS-MSP) assay which can detect methylated DNA (met-DNA) in serum with high sensitivity. To examine its prognostic value, we applied this new assay to the detection of met-DNA in serum of breast cancer patients. METHODS Serum samples taken before surgery from 336 primary invasive breast cancer patients were subjected to the OS-MSP assay for the promoter regions of GSTP1, RASSF1A, and RARβ2. The assay outcome was considered positive when methylation was detected in at least one of these three genes. Total DNA content in serum was also determined. RESULTS Of the 336 stage I/II patients, 33 (10%) were positive for met-DNA in serum and showed a significantly worse overall survival (OS) rate at 100 months (78 vs. 95%; p = 0.002) than those with negative findings (n = 303). Patients with high total DNA in serum (n = 112) also showed a significantly worse OS rate at 100 months (86 vs. 97%; p = 0.001) than those with low total DNA in serum (n = 224). Moreover, patients both positive for met-DNA and with high total DNA in serum (n = 18) showed a much worse OS rate at 100 months (65 vs. 94%; p < 0.001) than the others (n = 318). CONCLUSIONS Met-DNA in serum detected with the OS-MSP assay constitutes a significant and independent prognostic factor, and its combination with total DNA in serum seems to be even more effective for prediction of prognosis for breast cancer patients.
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Affiliation(s)
- Noriko Fujita
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
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Li L, Choi JY, Lee KM, Sung H, Park SK, Oze I, Pan KF, You WC, Chen YX, Fang JY, Matsuo K, Kim WH, Yuasa Y, Kang D. DNA methylation in peripheral blood: a potential biomarker for cancer molecular epidemiology. J Epidemiol 2012; 22:384-94. [PMID: 22863985 PMCID: PMC3798632 DOI: 10.2188/jea.je20120003] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aberrant DNA methylation is associated with cancer development and progression. There are several types of specimens from which DNA methylation pattern can be measured and evaluated as an indicator of disease status (from normal biological process to pathologic condition) and even of pharmacologic response to therapy. Blood-based specimens such as cell-free circulating nucleic acid and DNA extracted from leukocytes in peripheral blood may be a potential source of noninvasive cancer biomarkers. In this article, we describe the characteristics of blood-based DNA methylation from different biological sources, detection methods, and the factors affecting DNA methylation. We provide a comprehensive literature review of blood-based DNA methylation as a cancer biomarker and focus on the study of DNA methylation using peripheral blood leukocytes. Although DNA methylation patterns measured in peripheral blood have great potential to be useful and informative biomarkers of cancer risk and prognosis, large systematic and unbiased prospective studies that consider biological plausibility and data analysis issues will be needed in order to develop a clinically feasible blood-based assay.
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Affiliation(s)
- Lian Li
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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Schwarzenbach H. Circulating nucleic acids and protease activities in blood of tumor patients. Expert Opin Biol Ther 2012; 12 Suppl 1:S163-9. [DOI: 10.1517/14712598.2012.674508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Rykova EY, Morozkin ES, Ponomaryova AA, Loseva EM, Zaporozhchenko IA, Cherdyntseva NV, Vlassov VV, Laktionov PP. Cell-free and cell-bound circulating nucleic acid complexes: mechanisms of generation, concentration and content. Expert Opin Biol Ther 2012; 12 Suppl 1:S141-53. [PMID: 22500614 DOI: 10.1517/14712598.2012.673577] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Extracellular nucleic acids are found in human blood and cell culture medium as cell-free or being adsorbed at cell surface. In the last years, the circulating extracellular nucleic acids in blood were shown to be associated with certain diseases. Attempts are made to develop non-invasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. AREAS COVERED This article reviews accumulating data regarding cell-free and cell-surface-bound extracellular nucleic acid nature and generation mechanisms. Their existence as a constituent of the naturally occurring complexes with proteins or membrane-bearing particles is discussed with regard to their homeostatic concentration and distribution in healthy donor blood which are significantly altered in cancer patients. Gene-target and whole-genome studies reveal significant differences in gene representation between extracellular DNA and genome DNA. Overrepresentation of regions with high transcription activity has led to proposal that extracellular DNA generation is strongly dependent on the parent genome functionality, which is associated with chromosome packaging and DNA methylation levels. EXPERT OPINION Recent studies provide evidence of the circulating nucleome organization complexity indicating that discovery of extracellular DNA generation and circulation patterns in healthy condition and cancer is essential to enable the development of proper approaches for the selection of valid diagnostic markers.
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Affiliation(s)
- Elena Y Rykova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Acad. Lavrentyev Prosp., Novosibirsk, Russia.
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Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
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Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
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van Schooneveld E, Wouters MC, Van der Auwera I, Peeters DJ, Wildiers H, Van Dam PA, Vergote I, Vermeulen PB, Dirix LY, Van Laere SJ. Expression profiling of cancerous and normal breast tissues identifies microRNAs that are differentially expressed in serum from patients with (metastatic) breast cancer and healthy volunteers. Breast Cancer Res 2012; 14:R34. [PMID: 22353773 PMCID: PMC3496152 DOI: 10.1186/bcr3127] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/21/2011] [Accepted: 02/21/2012] [Indexed: 12/13/2022] Open
Abstract
Introduction MicroRNAs (miRNAs) are a group of small noncoding RNAs involved in the regulation of gene expression. As such, they regulate a large number of cellular pathways, and deregulation or altered expression of miRNAs is associated with tumorigenesis. In the current study, we evaluated the feasibility and clinical utility of circulating miRNAs as biomarkers for the detection and staging of breast cancer. Methods miRNAs were extracted from a set of 84 tissue samples from patients with breast cancer and eight normal tissue samples obtained after breast-reductive surgery. After reverse transcription and preamplification, 768 miRNAs were profiled by using the TaqMan low-density arrays. After data normalization, unsupervised hierarchical cluster analysis (UHCA) was used to investigate global differences in miRNA expression between cancerous and normal samples. With fold-change analysis, the most discriminating miRNAs between both tissue types were selected, and their expression was analyzed on serum samples from 20 healthy volunteers and 75 patients with breast cancer, including 16 patients with untreated metastatic breast cancer. miRNAs were extracted from 200 μl of serum, reverse transcribed, and analyzed in duplicate by using polymerase chain reaction (qRT-PCR). Results UHCA showed major differences in miRNA expression between tissue samples from patients with breast cancer and tissue samples from breast-reductive surgery (P < 0.0001). Generally, miRNA expression in cancerous samples tends to be repressed when compared with miRNA expression in healthy controls (P = 0.0685). The four most discriminating miRNAs by fold-change (miR-215, miR-299-5p, miR-411, and miR-452) were selected for further analysis on serum samples. All miRNAs at least tended to be differentially expressed between serum samples from patients with cancer and serum samples from healthy controls (miR-215, P = 0.094; miR-299-5P, P = 0.019; miR-411, P = 0.002; and miR-452, P = 0.092). For all these miRNAs, except for miR-452, the greatest difference in expression was observed between serum samples from healthy volunteers and serum samples from untreated patients with metastatic breast cancer. Conclusions Our study provides a basis for the establishment of miRNAs as biomarkers for the detection and eventually staging of breast cancer through blood-borne testing. We identified and tested a set of putative biomarkers of breast cancer and demonstrated that altered levels of these miRNAs in serum from patients with breast cancer are particularly associated with the presence of metastatic disease.
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Affiliation(s)
- Eleni van Schooneveld
- Department of Oncology, University Hospitals Leuven and Catholic University Leuven, Herestraat 49, Leuven, B3000 Belgium.
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Pan S, Xia W, Ding Q, Shu Y, Xu T, Geng Y, Lu Y, Chen D, Xu J, Wang F, Zhao C, Huang P, Huang P, Shen H, Hu Z, Lu S. Can plasma DNA monitoring be employed in personalized chemotherapy for patients with advanced lung cancer? Biomed Pharmacother 2012; 66:131-7. [PMID: 22401927 DOI: 10.1016/j.biopha.2011.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 11/08/2011] [Indexed: 02/08/2023] Open
Abstract
Personalized chemotherapy is the ideal treatment usually chosen to help improve the survival chances of patients with advanced lung cancer. However, there is no short-term evaluation protocol for predicting the efficacy of the therapy. The aim of this study was to determine the value of using plasma DNA to monitor chemotherapeutic efficacy and to select most appropriate chemotherapeutic regimen for patients with advanced lung cancer. Eighty-eight lung cancer patients and 200 healthy controls were included in this study. Plasma DNA was extracted from plasma samples with internal controls by using the BILATEST DNA Kit. The quantity of plasma DNA was determined by using duplex real-time quantitative PCR. After first-line chemotherapy, plasma DNA levels of partial response patients were significantly different from those of stable disease patients or progressive disease patients, but with no statistical difference from healthy controls (P=0.014, P<0.001 and P=0.418, respectively). Survival analysis showed a statistically better survival time in patients who had lower levels of plasma DNA after the third cycle chemotherapy (P=0.031). In this study, the correlation of the kinetics of DNA concentrations with chemotherapeutic efficacy during the whole therapy was also observed. The quantification of plasma DNA is a sensitive indicator of chemotherapeutic efficacy in advanced lung cancer patients, and it can be useful in predicting response to therapy and guiding medication.
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Affiliation(s)
- Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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