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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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Savli H, Sertdemir N, Aydin D, Dursun B, Kurtas O, Reka S, Sunnetci-Akkoyunlu D, Eren-Keskin S, Uygun K, Ozden E, Isik U, Cabuk D, Demir G, Guzdolu E, Gokbayrak M, Aksu MG, Canturk NZ, Cine N. TP53, EGFR and PIK3CA gene variations observed as prominent biomarkers in breast and lung cancer by plasma cell-free DNA genomic testing. J Biotechnol 2019; 300:87-93. [DOI: 10.1016/j.jbiotec.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/08/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023]
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Clinical implications of circulating cell-free DNA quantification and metabolic tumor burden in advanced non-small cell lung cancer. Lung Cancer 2019; 134:158-166. [PMID: 31319975 DOI: 10.1016/j.lungcan.2019.06.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/10/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This study unravels the significance of cell-free DNA (cfDNA) quantification as a promising measure of the biological behavior/aggressiveness of tumors. Metabolic tumor volume (MTV) and total lesion glycolysis (TLG) measured by positron emission tomography/computed tomography scan enable a precise assessment of metabolic tumor burden. However, their clinical implications in identifying patients who need more aggressive treatment in advanced non-small cell lung cancer (NSCLC) are not fully understood. MATERIALS AND METHODS In the current prospective trial, we analyzed 101 newly diagnosed advanced NSCLC (stage III-IV) patients with measurable baseline MTV, TLG, and cfDNA quantification. The best cut-offs for cfDNA levels, MTV, and TLG to predict progression-free survival and overall survival were determined using X-tile analysis. RESULTS There were significant positive correlations between cfDNA and MTV (r = 0.488, p < 0.001) and between cfDNA and TLG (r = 0.554, p < 0.001). High-cfDNA levels and high-MTV/TLG negatively correlated with overall survival (OS) (all p < 0.001). Patients with high-MTV showed similar median OS irrespective of their cfDNA levels (low-cfDNA vs. high-cfDNA=9.2 vs 6.6 months; p > 0.05). However, patients with low-MTV and low-cfDNA levels showed longer OS than those with low-MTV and high-cfDNA levels (low-cfDNA vs. high-cfDNA=49.3 vs 11.5 months; p < 0.001). The patient group with low-TLG also showed similar trends. The cfDNA level was an independent prognostic factor for OS by Cox-proportional hazard analysis. CONCLUSION Although the patients with high metabolic tumor burden had a poor prognosis, regardless of the biological behavior/aggressiveness of the tumor, patients with low metabolic tumor burden and high cfDNA levels showed a poor prognosis. Taken together, this study indicates a stronger prognostic value of baseline cfDNA levels in identifying patients with advanced NSCLC and personalizing their treatment strategies for better survival.
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Mirtavoos-Mahyari H, Ghafouri-Fard S, Khosravi A, Motevaseli E, Esfahani-Monfared Z, Seifi S, Salimi B, Oskooei VK, Ghadami M, Modarressi MH. Circulating free DNA concentration as a marker of disease recurrence and metastatic potential in lung cancer. Clin Transl Med 2019; 8:14. [PMID: 31001798 PMCID: PMC6473013 DOI: 10.1186/s40169-019-0229-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/06/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Plasma circulating cell-free (cf) DNA is regarded as a source of tumor DNA. Based on availability of blood tissue for the purposes of early detection of cancer and patients' follow-up, several studies have evaluated concentration of cf DNA in cancer patients in association with tumor features. In the present study, we assessed concentration of cf DNA in lung cancer patients with two commercial kits (MN and QIAGEN) to find whether it can be used as a prognostic biomarker. RESULTS Primary cf DNA concentrations as measured by QIAGEN kit was significantly higher in patients who died in the follow-up period compared with alive patients (P = 0.007). Moreover, the concentrations as measured by both methods were higher in patients who experienced recurrence in the follow-up period compared with patients without recurrence (P = 0.008 and 0.007 for MN and QIAGEN kits respectively). Significant associations were also found between cf DNA concentrations and tumor stage (P = 0.005 and 0.02 for MN and QIAGEN kits respectively). Notably, cf DNA concentration was higher in metastatic tumors compared with non-metastatic tumors in association with number of involved organs. Based on the AUC values, both kits could differentiate metastatic cancers from non-metastatic ones with accuracy of 98%. CONCLUSIONS The current study highlights the accuracy of cf DNA concentrations for prediction of disease course in lung cancer patients.
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Affiliation(s)
- Hanifeh Mirtavoos-Mahyari
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adnan Khosravi
- Tobacco Prevention and Control Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elahe Motevaseli
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Esfahani-Monfared
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sharareh Seifi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Babak Salimi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi Oskooei
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Ghadami
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Woff E, Kehagias P, Vandeputte C, Ameye L, Guiot T, Paesmans M, Hendlisz A, Flamen P. Combining 18F-FDG PET/CT-Based Metabolically Active Tumor Volume and Circulating Cell-Free DNA Significantly Improves Outcome Prediction in Chemorefractory Metastatic Colorectal Cancer. J Nucl Med 2019; 60:1366-1372. [PMID: 30850494 DOI: 10.2967/jnumed.118.222919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 02/11/2019] [Indexed: 12/26/2022] Open
Abstract
Baseline whole-body metabolically active tumor volume (WB-MATV) measured by 18F-FDG PET/CT and circulating cell-free DNA (cfDNA) have been separately validated as predictors of overall and progression-free survival (OS/PFS) in chemorefractory metastatic colorectal cancer (mCRC) patients. This study assessed the correlation between WB-MATV and cfDNA, evaluating the added prognostic value of these in combination, along with clinical parameters. Methods: Of 141 mCRC patients included in a prospective multicenter trial, 132 were evaluable for OS/PFS. cfDNA was extracted from 3 mL of plasma and quantified using a fluorometer. All target lesions were delineated on 18F-FDG PET/CT, and their metabolic volumes were summed to obtain the WB-MATV. Results: Baseline WB-MATV and cfDNA were strongly correlated (r = 0.70; P < 0.001) but showed discordance in 23 of 132 (17%) patients. A multivariate analysis identified 3 independent negative predictors of PFS (high cfDNA, short time since diagnosis, and body mass index < 30) and 5 of OS (high cfDNA, high WB-MATV, body mass index < 30, poor performance status, and short time since diagnosis). Combining WB-MATV and cfDNA increased the overall prognostic value and allowed identification of a subgroup of patients with low cfDNA and high WB-MATV who were associated with intermediate survival (median OS of 8.1 for low-cfDNA/high-MATV patients vs. 12.7 mo for low-cfDNA/low-MATV patients; hazard ratio, 2.04; P = 0.02). Conclusion: This study confirms the added prognostic value of combined circulating cfDNA and PET-based WB-MATV in chemorefractory mCRC patients. The combination of these two biomarkers should provide a firm basis for risk stratification, both in clinical practice and in research trials.
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Affiliation(s)
- Erwin Woff
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pashalina Kehagias
- Gastro-Oncology Translational Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Caroline Vandeputte
- Gastro-Oncology Translational Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Lieveke Ameye
- Data Centre, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium; and
| | - Thomas Guiot
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marianne Paesmans
- Data Centre, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium; and
| | - Alain Hendlisz
- Medical Oncology Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick Flamen
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Saarenheimo J, Eigeliene N, Andersen H, Tiirola M, Jekunen A. The Value of Liquid Biopsies for Guiding Therapy Decisions in Non-small Cell Lung Cancer. Front Oncol 2019; 9:129. [PMID: 30891428 PMCID: PMC6411700 DOI: 10.3389/fonc.2019.00129] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/13/2019] [Indexed: 12/15/2022] Open
Abstract
Targeted therapies have allowed for an individualized treatment approach in non-small-cell lung cancer (NSCLC). The initial therapeutic decisions and success of targeted therapy depend on genetic identification of personal tumor profiles. Tissue biopsy is the gold standard for molecular analysis, but non-invasive or minimally invasive liquid biopsy methods are also now used in clinical practice, allowing for later monitoring and optimization of the cancer treatment. The inclusion of liquid biopsy in the management of NSCLC provides strong evidence on early treatment response, which becomes a basis for determining disease progression and the need for changes in treatment. Liquid biopsies can drive the decision making for treatment strategies to achieve better patient outcomes. Cell-free DNA and circulating tumor cells obtained from the blood are promising markers for determining patient status. They may improve cancer treatments, allow for better treatment control, enable early interventions, and change decision making from reactive actions toward more predictive early interventions. This review aimed to present current knowledge on and the usefulness of liquid biopsy studies in NSCLC from the perspective of how it has allowed individualized treatments according to gene profiling and how the method may alter the treatment decisions in the future.
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Affiliation(s)
- Jatta Saarenheimo
- Department of Pathology, Vasa Central Hospital, Vaasa, Finland.,Department of Biological and Environmental Science, Nano Science Center, University of Jyväskylä, Jyväskylä, Finland
| | - Natalja Eigeliene
- Department of Oncology, Vasa Central Hospital, Vaasa, Finland.,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland
| | - Heidi Andersen
- Department of Pulmonology, Vasa Central Hospital, Vaasa, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nano Science Center, University of Jyväskylä, Jyväskylä, Finland
| | - Antti Jekunen
- Department of Oncology, Vasa Central Hospital, Vaasa, Finland.,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland
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57
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Ye Z, Wang C, Wan S, Mu Z, Zhang Z, Abu-Khalaf MM, Fellin FM, Silver DP, Neupane M, Jaslow RJ, Bhattacharya S, Tsangaris TN, Chervoneva I, Berger A, Austin L, Palazzo JP, Myers RE, Pancholy N, Toorkey D, Yao K, Krall M, Li X, Chen X, Fu X, Xing J, Hou L, Wei Q, Li B, Cristofanilli M, Yang H. Association of clinical outcomes in metastatic breast cancer patients with circulating tumour cell and circulating cell-free DNA. Eur J Cancer 2019; 106:133-143. [PMID: 30528798 PMCID: PMC6347110 DOI: 10.1016/j.ejca.2018.10.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/03/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Both circulating tumour cell (CTC) and total circulating cell-free DNA (ccfDNA) predict cancer patient prognosis. However, no study has explored the prognostic value of the combined use of CTC and ccfDNA. We aimed to investigate individual and joint effects of CTC and ccfDNA on clinical outcomes of metastatic breast cancer (MBC) patients. METHODS We collected 227 blood samples from 117 MBC patients. CTCs were enumerated using the CellSearch System. ccfDNAs were quantified by quantitative real-time polymerase chain reaction and Qubit fluorometer. The individual and joint effects of CTC and ccfDNA levels on patient progression-free survival (PFS) and overall survival (OS) were analysed using Cox proportional hazards models. RESULTS Compared to patients with <5 CTCs, patients with ≥5 CTCs had a 2.58-fold increased risk of progression and 3.63-fold increased risk of death. High level of ccfDNA was associated with a 2.05-fold increased risk of progression and 3.56-fold increased risk of death. These associations remained significant after adjusting for other important clinical covariates and CTC/ccfDNA levels. CTC and ccfDNA levels had a joint effect on patient outcomes. Compared to patients with low levels of both CTC and ccfDNA, those with high levels of both markers exhibited a >17-fold increased death risk (P < 0.001). Moreover, longitudinal analysis of 132 samples from 22 patients suggested that the inconsistency between CTC level and outcome in some patients could possibly be explained by ccfDNA level. CONCLUSIONS CTC and total ccfDNA levels were individually and jointly associated with PFS and OS in MBC patients.
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Affiliation(s)
- Zhong Ye
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Chun Wang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Shaogui Wan
- Institute of Pharmacy, Pharmaceutical College, Henan University, Kaifeng, Henan 475004, China
| | - Zhaomei Mu
- Department of Medicine, Division of Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zhenchao Zhang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Maysa M Abu-Khalaf
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Frederick M Fellin
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Daniel P Silver
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Manish Neupane
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Rebecca J Jaslow
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Saveri Bhattacharya
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Theodore N Tsangaris
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Inna Chervoneva
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Adam Berger
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Laura Austin
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Juan P Palazzo
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ronald E Myers
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Neha Pancholy
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Darayus Toorkey
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Kaelan Yao
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Max Krall
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Xiuling Li
- Department of Gastroenterology, People's Hospital of Henan Province, Zhengzhou, Henan 450003, China
| | - Xiaobing Chen
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Xiuhong Fu
- Center for Reproductive Medicine and Genetics, Central Hospital of Luohe, Luohe, Henan 462300, China
| | - Jinliang Xing
- Experimental Teaching Center, School of Basic Medicine, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Qiang Wei
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Bingshan Li
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Hushan Yang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Lin LH, Chang KW, Kao SY, Cheng HW, Liu CJ. Increased Plasma Circulating Cell-Free DNA Could Be a Potential Marker for Oral Cancer. Int J Mol Sci 2018; 19:ijms19113303. [PMID: 30352977 PMCID: PMC6274798 DOI: 10.3390/ijms19113303] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Oral squamous cell carcinoma (OSCC) is a disease that affects patients worldwide. DNA of dead cells is released into the blood stream and may be isolated from plasma or serum samples. This DNA is termed cell-free DNA (cfDNA). cfDNA is increased in several types of malignancies. We investigated if there was a correlation between cfDNA levels and the progression of OSCC. Methods: Using quantitative spectrometry, we measured plasma cfDNA in 121 patients with OSCC and 50 matched controls. Mann Whitney and Wilcoxon tests were used to compare differences among various clinical variants. Receiver operating characteristic (ROC) analysis was used to obtain levels suitable for the separation of the clinical subsets. Kaplan-Meier analysis was used to assess correlation with survival. Results: Plasma cfDNA was significantly elevated in patients with OSCC relative to controls. Plasma cfDNA levels correlated with larger tumor size, cervical lymph node metastasis and late stage. Higher plasma cfDNA levels were associated with a poor prognosis of OSCC, which is a new finding. Conclusion: Plasma cfDNA could serve as a novel and easily accessible biomarker in OSCC, providing diagnostic and prognostic value.
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Affiliation(s)
- Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Stomatology, Medical Education and Research, Veterans General Hospital, Taipei 11217, Taiwan.
| | - Shou-Yen Kao
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Stomatology, Medical Education and Research, Veterans General Hospital, Taipei 11217, Taiwan.
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan.
| | - Chung-Ji Liu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Oral and Maxillofacial Surgery, Taipei MacKay Memorial Hospital, Taipei 10449, Taiwan.
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Wu J, Tang W, Huang L, Hou N, Wu J, Cheng X, Ma D, Qian P, Shen Q, Guo W, Peng W, Liu Y, Jiang C, Feng J. The analysis of cell-free DNA concentrations and integrity in serum of initial and treated of lymphoma patients. Clin Biochem 2018; 63:59-65. [PMID: 30292543 DOI: 10.1016/j.clinbiochem.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/13/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To evaluate cell-free DNA (cfDNA) in plasma as a promising biomarker for lymphoma, altered levels of cfDNA and its association with clinical parameters are investigated in patients suffered from lymphomas. METHODS Peripheral blood specimens were collected from 60 patients with lymphoma during initial diagnosis and those of another 107 patients with lymphoma during treated stage were also collected, 93 healthy volunteers were selected as control group. Quantitative PCR was used to detect cfDNA level in each group, cfDNA level in different groups was analyzed to understand its relationship with lymphoma patients' clinical features. After correlation analysis between cfDNA and clinical characteristics, Receiver operator characteristic curve was performed to analyze sensitivity and specificity of cfDNA and LDH. RESULTS cfDNA concentration and integrity in initial stage of lymphoma patients were significantly higher than those in treated stage, and cfDNA concentration in treated phase was significantly higher than cfDNA concentration in control group. There was no significant difference in cfDNA integrity at treated stage compared with control group. There was no significant correlation between patient's age, gender, extranodal invasion and lymphoma pathological type and cfDNA concentration and integrity; In contrast, there was a significant correlation between ECOG score, LDH content, Ann Arbor stage, IPI, B-symptoms, Ki-67 expression and radiotherapy and cfDNA concentration and integrity, both at the time of initial diagnosis and treated stage. cfDNA concentration detection is an optimal diagnostic indicator, followed by cfDNA integrity detection, the sensitivity and specificity of both are superior to the traditional LDH detection. CONCLUSION cfDNA level is significantly increased in lymphomas patient plasma and may help lymphoma screening. cfDNA level may serve as a potential indicator of lymphomas treatment efficacy.
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Affiliation(s)
- Jianqiu Wu
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Weiyan Tang
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Laiquan Huang
- Department of Hematology, The First Affiliated Hospital of Wannan Medical College, No.2, Zheshan West Road, Wuhu City 241001, Anhui Province, China
| | - Ning Hou
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Jing Wu
- Soochow University, No.1, Shizi Street, Suzhou city 215006, Jiangsu Province, China
| | - Xianfeng Cheng
- Clinic laboratory of Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences, No.12, Jiangwangmiao Street, Xuanwu District, Nanjing City 210042, Jiangsu Province, China
| | - Dawei Ma
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Pudong Qian
- Department of Radiotherapy, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Qian Shen
- Department of Medical Oncology, Nantong Tumor Hospital, No.48, Qingnian West Road, Nantong city 226000, Jiangsu Province, China
| | - Wenjie Guo
- Department of Radiotherapy, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Wei Peng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Yufei Liu
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Cunshun Jiang
- Department of Medical Oncology, Lanxi County People's Hospital. No.65, North Street of Langxi County, 242100, Anhui Province, China
| | - Jifeng Feng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China.
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Lee Y, Park S, Kim WS, Lee JC, Jang SJ, Choi J, Choi C. Correlation between progression-free survival, tumor burden, and circulating tumor DNA in the initial diagnosis of advanced-stage EGFR-mutated non-small cell lung cancer. Thorac Cancer 2018; 9:1104-1110. [PMID: 29989342 PMCID: PMC6119619 DOI: 10.1111/1759-7714.12793] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND This study was conducted to identify whether the presence of circulating tumor DNA (ctDNA) in plasma before treatment with EGFR-tyrosine kinase inhibitors (TKIs) is associated with clinical outcomes. METHODS Fifty-seven pairs of tissues and plasma samples were obtained from patients with NSCLC adenocarcinoma harboring activating EGFR mutations before the administration of EGFR-TKI treatment. ctDNA mutation was identified using the PANAMutyper EGFR mutation kit. Both qualitative and quantitative analyzes of the data were performed. RESULTS Concordance rates with tissue biopsy were 40.4% and 59.6% for the qualitative and quantitative methods, respectively. Bone metastasis showed a statistically significant correlation with ctDNA detection (odds ratio 3.985, 95% confidence interval [CI] 1.027-15.457; P = 0.046). Progression-free survival (PFS) was significantly shorter in the group detected with ctDNA than in the undetected ctDNA group (median PFS 9.8 vs. 20.7 months; hazard ratio [HR] 2.30, 95% CI 1.202-4.385; P = 0.012). Detection of ctDNA before treatment with EGFR-TKIs (HR 2.388, 95% CI 1.138-5.014; P = 0.021) and extra-thoracic lymph node metastasis (HR 13.533, 95% CI 2.474-68.747; P = 0.002) were independently associated with PFS. Six of 11 patients (45.5%) monitored by serial sampling showed a dynamic change in ctDNA prior to disease progression. CONCLUSION Quantitative testing can increase the sensitivity of the ctDNA detection test. Patients with detectable ctDNA had significantly shorter PFS after receiving EGFR-TKIs than those with undetectable ctDNA. Tumor burden may be associated with plasma ctDNA detection. A shorter PFS was associated with detection of ctDNA and extra-thoracic lymph node metastasis. Dynamic changes in the ctDNA level may help predict clinical outcomes.
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Affiliation(s)
- Yunkyoung Lee
- Department of Pulmonary and Critical Care MedicineChungnam National University HospitalDaejeonSouth Korea
| | - Sojung Park
- Department of Pulmonary and Critical Care Medicine, Hallym University Medical CenterUniversity of Hallym College of MedicineKangwonKorea
| | - Woo Sung Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Se Jin Jang
- Department of Pathology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Jene Choi
- Department of Pathology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Chang‐Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
- Department of Oncology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
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61
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Demuth C, Spindler KLG, Johansen JS, Pallisgaard N, Nielsen D, Hogdall E, Vittrup B, Sorensen BS. Measuring KRAS Mutations in Circulating Tumor DNA by Droplet Digital PCR and Next-Generation Sequencing. Transl Oncol 2018; 11:1220-1224. [PMID: 30086420 PMCID: PMC6085225 DOI: 10.1016/j.tranon.2018.07.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/23/2018] [Indexed: 12/22/2022] Open
Abstract
Measuring total cell-free DNA (cfDNA) or cancer-specific mutations herein has presented as new tools in aiding the treatment of cancer patients. Studies show that total cfDNA bears prognostic value in metastatic colorectal cancer (mCRC) and that measuring cancer-specific mutations could supplement biopsies. However, limited information is available on the performance of different methods. Blood samples from 28 patients with mCRC and known KRAS mutation status were included. cfDNA was extracted and quantified with droplet digital polymerase chain reaction (ddPCR) measuring Beta-2 Microglobulin. KRAS mutation detection was performed using ddPCR (Bio-Rad) and next-generation sequencing (NGS, Ion Torrent PGM). Comparing KRAS mutation status in plasma and tissue revealed concordance rates of 79% and 89% for NGS and ddPCR. Strong correlation between the methods was observed. Most KRAS mutations were also detectable in 10-fold diluted samples using the ddPCR. We find that for detection of KRAS mutations in ctDNA ddPCR was superior to NGS both in analysis success rate and concordance to tissue. We further present results indicating that lower amount of plasma may be used for detection of KRAS mutations in mCRC.
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Affiliation(s)
- Christina Demuth
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | - Julia S Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Niels Pallisgaard
- Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Dorte Nielsen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Estrid Hogdall
- Department of Pathology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Benny Vittrup
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
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62
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Wang X, Wang L, Su Y, Yue Z, Xing T, Zhao W, Zhao Q, Duan C, Huang C, Zhang D, Jin M, Cheng X, Chen S, Liu Y, Ma X. Plasma cell-free DNA quantification is highly correlated to tumor burden in children with neuroblastoma. Cancer Med 2018; 7:3022-3030. [PMID: 29905010 PMCID: PMC6051223 DOI: 10.1002/cam4.1586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/13/2022] Open
Abstract
To evaluate plasma cell-free DNA (cfDNA) as a promising biomarker for neuroblastoma (NB) tumor burden. Seventy-nine eligible patients with newly diagnosed NB were recruited from Beijing Children's Hospital between April 2016 and April 2017. Additionally, from September 2011 to June 2017, 79 patients with stable NB were evaluated with a median follow-up time of 21 months. Approximately 2 mL of peripheral blood was drawn upon enrollment, and plasma cfDNA levels were measured via quantitative polymerase chain reaction (qPCR). Total cfDNA analysis was performed using the long interspersed nuclear element 1 (LINE-1) 79 bp fragment, and DNA integrity was calculated by the ratio of the LINE-1 300 bp fragment to the LINE-1 79 bp fragment. A total of 79 NB patients with a median age of 36 months comprised the group of newly diagnosed NB patients. The main primary tumor site was the retroperitoneal and adrenal region (81%). Three or more metastatic sites were found in 17.7% of patients. Stable NB patients older than 18 months comprised 98.7% of the stable NB patients. Neuron-specific enolase (NSE), lactate dehydrogenase (LDH), and cfDNA levels were dramatically increased in the newly diagnosed NB patients and significantly different from those in the stable NB patients. Moreover, the concentration of cfDNA was much higher in patients with larger tumors. By analyzing the area under the receiver operator characteristic (ROC) curve (AUC), the areas of total cfDNA, NSE, and LDH levels were 0.953, 0.929, and 0.906, respectively. The sensitivity and specificity data clarified that the level of circulating cfDNA in plasma can be considered as a reliable biomarker for describing tumor load in NB. The plasma cfDNA concentration was as good as the levels of LDH and NSE to discriminate the tumor burden in children with NB.
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Affiliation(s)
- Xisi Wang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Lijun Wang
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Yan Su
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Zhixia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tianyu Xing
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Wen Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Qian Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chao Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Cheng Huang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Dawei Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Mei Jin
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xianfeng Cheng
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Shenglan Chen
- Taizhou Genewill Medical Laboratory Company Limited, Pharmaceutics City of China, Taizhou, Jiangsu, China
| | - Yi Liu
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Xiaoli Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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63
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Cabanero M, Tsao MS. Circulating tumour DNA in EGFR-mutant non-small-cell lung cancer. ACTA ACUST UNITED AC 2018; 25:S38-S44. [PMID: 29910646 DOI: 10.3747/co.25.3761] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of targeted therapy in non-small-cell lung cancer (nsclc) has made the routine molecular diagnosis of EGFR mutations crucial for optimal patient management. Obtaining tumour tissue for biomarker testing, especially in the setting of re-biopsy, can present many challenges. A potential alternative source of tumour dna is circulating cell-free tumour-derived dna (ctdna). Although ctdna is present in low quantities in plasma, the convenience of sample acquisition and the increasing reliability of detection methods make this approach a promising one. The various performance characteristics of both digital and nondigital platforms are still variable, and a standardized approach is needed that will make those platforms reliable clinical tools for the detection of EGFR sensitizing mutations and resistance mutations, including the T790M resistance mutation. Information derived from ctdna can be used to assess tumour burden, to identify genomic-based resistance mechanisms, and to track dynamic changes during therapy.
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Affiliation(s)
- M Cabanero
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - M S Tsao
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
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Yang N, Li Y, Liu Z, Qin H, Du D, Cao X, Cao X, Li J, Li D, Jiang B, Duan L, Yang H, Zhang Z, Lin H, Li J, Yang Z, Xiong L, Shen H, Lin L, Li F. The characteristics of ctDNA reveal the high complexity in matching the corresponding tumor tissues. BMC Cancer 2018; 18:319. [PMID: 29566644 PMCID: PMC5865353 DOI: 10.1186/s12885-018-4199-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/08/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and corresponding tumor tissues. Our goal was to systematically investigate the critical factors contributing to different concordance between ctDNA and corresponding tumor tissues. METHODS We recruited two groups of IIIB or IV lung cancer patients: The standard group to evaluate the accuracy of our method and the concordance between ctDNA and tumor tissues, and the study group with various clinical conditions. We applied our unique identification (UID) indexed capturing-based sequencing (UC-Seq) to ctDNA samples, and confirm the results by Droplet digital PCR (ddPCR). RESULTS Considering mutations detected from NGS of tumor tissues as golden standard, UC-Seq achieved overall 93.6% sensitivity for SNVs and Indels, and 0.8 Pearson correlation between tumor TMB and bTMB. Efficacious treatments, long sampling date (more than 2 weeks) between tumor tissues and ctDNA and low concentrations of cfDNA (less than 9 ng/ml) could significantly decrease the concordance between ctDNA and tumor tissues. About 84% mutations showed shorter mutant fragment length than that of wild-type fragments, and the AFs of mutations could be significantly enriched in small-size ctDNA. CONCLUSIONS In late-stage lung cancer patients, ctDNA generally has high concordance with tumor tissues. However it could be significantly affected by three clinical conditions which could dynamically change the content of ctDNA. Moreover, the detection limit could be further extended by enriching small-size ctDNA in the preparation of samples.
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Affiliation(s)
- Nong Yang
- Lung Cancer and Gastrointestinal Unit, Department of Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Yi Li
- Department of Oncology, Yunnan Province Traditional Chinese Medicine Hospital, Kunming, China
| | - Zhidong Liu
- Second Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hao Qin
- The Research and Development Institute of Precision Medicine, 3D Medicine Inc, Shanghai, China
| | - Duanming Du
- Department of Interventional Radiology, Shenzhen Second People’s Hospital (First Hospital of Shenzhen University), Shenzhen, China
| | - Xinkai Cao
- The Research and Development Institute of Precision Medicine, 3D Medicine Inc, Shanghai, China
| | - Xiaoqing Cao
- Second Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jun Li
- Department of Oncology, Yunnan Province Traditional Chinese Medicine Hospital, Kunming, China
| | - Dongge Li
- Department of Oncology, Yunnan Province Traditional Chinese Medicine Hospital, Kunming, China
| | - Bo Jiang
- Department of Cadre’s Medical Oncology, The Third Affiliated Hospital of Kunming Medical University(Yunnan Cancer Hospital), Kunming, China
| | - Lincan Duan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Haiyan Yang
- Lung Cancer and Gastrointestinal Unit, Department of Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Zhenghua Zhang
- Department of oncology, Jing’An District Centre Hospital of Shanghai (Huashan Hospital Fudan University Jing’An Branch), Shanghai, China
| | - Hao Lin
- Department of Oncology, Huashan Hospital north, Fudan University, Shanghai, China
| | - Jianying Li
- Department of Oncology, Nantong Tumor Hospital, Nantong, China
| | - Zhenhua Yang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lei Xiong
- The Research and Development Institute of Precision Medicine, 3D Medicine Inc, Shanghai, China
| | - Hua Shen
- Department of Oncology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Lizhu Lin
- Department of Oncology, First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Fugen Li
- The Research and Development Institute of Precision Medicine, 3D Medicine Inc, Shanghai, China
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65
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Buder A, Hochmair MJ, Schwab S, Bundalo T, Schenk P, Errhalt P, Mikes RE, Absenger G, Patocka K, Baumgartner B, Setinek U, Burghuber OC, Prosch H, Pirker R, Filipits M. Cell-Free Plasma DNA-Guided Treatment With Osimertinib in Patients With Advanced EGFR-Mutated NSCLC. J Thorac Oncol 2018; 13:821-830. [PMID: 29505901 DOI: 10.1016/j.jtho.2018.02.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/04/2018] [Accepted: 02/24/2018] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Osimertinib is standard treatment for patients with advanced EGFR T790M-mutated non-small-cell lung cancer who have been pre-treated with EGFR-tyrosine kinase inhibitors (TKIs). We studied whether cell-free plasma DNA for T790M detection can be used to select patients for osimertinib treatment in the clinical routine. METHODS From April 2015 to November 2016, we included 119 patients with advanced EGFR-mutated non-small-cell lung cancer who had progressed under treatment with an EGFR-TKI. The T790M mutation status was assessed in cell-free plasma DNA by droplet digital polymerase chain reaction in all patients and by tissue analyses in selected patients. RESULTS T790M mutations were detected in 85 (93%) patients by analyses of cell-free plasma DNA and in 6 (7%) plasma-negative patients by tumor re-biopsy. Eighty-nine of 91 T790M-positive patients received osimertinib. Median progression-free survival (PFS) was 10.1 months (95% confidence interval [CI]: 8.1-12.1). Median survival was not reached and the 1-year survival was 64%. The response rate was 70% in T790M-positive patients (n = 91) in the intention-to-treat population. PFS trended to be shorter in patients with high T790M copy number (≥10 copies/mL) compared to those with low T790M copy number (<10 copies/mL) (hazard ratio for PFS = 1.72, 95% CI: 0.92-3.2, p = 0.09). A comparable trend was observed for overall survival (hazard ratio for overall survival = 2.16, 95% CI: 0.89-5.25, p = 0.09). No difference in response rate was observed based on T790M copy numbers. CONCLUSION Plasma genotyping using digital polymerase chain reaction is clinically useful for the selection of patients who had progressed during first-line EGFR-TKI therapy for treatment with osimertinib.
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Affiliation(s)
- Anna Buder
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria
| | - Maximilian J Hochmair
- Department of Respiratory and Critical Care Medicine, and Ludwig Boltzmann Institute of COPD and Respiratory Epidemiology, Otto Wagner Hospital, Vienna, Austria
| | - Sophia Schwab
- Department of Respiratory and Critical Care Medicine, and Ludwig Boltzmann Institute of COPD and Respiratory Epidemiology, Otto Wagner Hospital, Vienna, Austria
| | | | - Peter Schenk
- Department of Pneumology, LKH Hochegg, Hochegg, Austria
| | - Peter Errhalt
- Department of Pneumology, University Hospital Krems, Krems, Austria
| | - Romana E Mikes
- Department of Pulmonary Medicine, University Clinic Salzburg, Salzburg, Austria
| | - Gudrun Absenger
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Kurt Patocka
- Department of Pneumology, Hietzing Hospital, Vienna, Austria
| | | | - Ulrike Setinek
- Department of Respiratory and Critical Care Medicine, and Ludwig Boltzmann Institute of COPD and Respiratory Epidemiology, Otto Wagner Hospital, Vienna, Austria
| | - Otto C Burghuber
- Department of Respiratory and Critical Care Medicine, and Ludwig Boltzmann Institute of COPD and Respiratory Epidemiology, Otto Wagner Hospital, Vienna, Austria
| | - Helmut Prosch
- Department of Radiology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Robert Pirker
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Martin Filipits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria.
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66
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Bennett CW, Berchem G, Kim YJ, El-Khoury V. Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget 2018; 7:71013-71035. [PMID: 27589834 PMCID: PMC5342606 DOI: 10.18632/oncotarget.11717] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022] Open
Abstract
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.
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Affiliation(s)
- Catherine W Bennett
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
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67
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Hench IB, Hench J, Tolnay M. Liquid Biopsy in Clinical Management of Breast, Lung, and Colorectal Cancer. Front Med (Lausanne) 2018; 5:9. [PMID: 29441349 PMCID: PMC5797586 DOI: 10.3389/fmed.2018.00009] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Examination of tumor molecular characteristics by liquid biopsy is likely to greatly influence personalized cancer patient management. Analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and tumor-derived exosomes, all collectively referred to as “liquid biopsies,” are not only a modality to monitor treatment efficacy, disease progression, and emerging therapy resistance mechanisms, but they also assess tumor heterogeneity and evolution in real time. We review the literature concerning the examination of ctDNA and CTC in a diagnostic setting, evaluating their prognostic, predictive, and monitoring capabilities. We discuss the advantages and limitations of various leading ctDNA/CTC analysis technologies. Finally, guided by the results of clinical trials, we discuss the readiness of cell-free DNA and CTC as routine biomarkers in the context of various common types of neoplastic disease. At this moment, one cannot conclude whether or not liquid biopsy will become a mainstay in oncology practice.
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Affiliation(s)
- Ivana Bratić Hench
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jürgen Hench
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Markus Tolnay
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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68
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Giroux Leprieur E, Herbretau G, Dumenil C, Julie C, Giraud V, Labrune S, Dumoulin J, Tisserand J, Emile JF, Blons H, Chinet T. Circulating tumor DNA evaluated by Next-Generation Sequencing is predictive of tumor response and prolonged clinical benefit with nivolumab in advanced non-small cell lung cancer. Oncoimmunology 2018; 7:e1424675. [PMID: 29721388 DOI: 10.1080/2162402x.2018.1424675] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Nivolumab is an anti-PD1 antibody, given in second-line or later treatment in advanced non-small cell lung cancer (NSCLC). The objective of this study was to describe the predictive value of circulating tumor DNA (ctDNA) on the efficacy of nivolumab in advanced NSCLC. We prospectively included all consecutive patients with advanced NSCLC treated with nivolumab in our Department between June 2015 and October 2016. Plasma samples were obtained before the first injection of nivolumab and at the first tumor evaluation with nivolumab. ctDNA was analyzed by Next-Generation Sequencing (NGS), and the predominant somatic mutation was followed for each patient and correlated with tumor response, clinical benefit (administration of nivolumab for more than 6 months), and progression-free survival (PFS). Of 23 patients, 15 had evaluable NGS results at both times of analysis. ctDNA concentration at the first tumor evaluation and ctDNA change correlated with tumor response, clinical benefit and PFS. ROC curve analyses showed good diagnostic performances for tumor response and clinical benefit, both for ctDNA concentration at the first tumor evaluation (tumor response: positive predictive value (PPV) at 100.0% and negative predictive value (NPV) at 71.0%; clinical benefit: PPV at 83.3% and NPV 77.8%) and the ctDNA change (tumor response: PPV 100.0% and NPV 62.5%; clinical benefit: PPV 100.0% and NPV 80.0%). Patients without ctDNA concentration increase >9% at 2 months had a long-term benefit of nivolumab. In conclusion, NGS analysis of ctDNA allows the early detection of tumor response and long-term clinical benefit with nivolumab in NSCLC.
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Affiliation(s)
- Etienne Giroux Leprieur
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France.,EA4340, Biomarqueursen Cancérologie et Onco-Hématologie, UVSQ, Paris-Saclay University, Boulogne-Billancourt, France
| | - Guillaume Herbretau
- INSERM UMR-S1147, CNRS SNC 5014, Saints-Pères Research Center, 45 rue des Saints-Pères Paris-Descartes University, Sorbonne Paris Cité University, Paris, France.,Department of Molecular Biology, Georges Pompidou European Hospital, 20 rue Leblanc, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Coraline Dumenil
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Catherine Julie
- EA4340, Biomarqueursen Cancérologie et Onco-Hématologie, UVSQ, Paris-Saclay University, Boulogne-Billancourt, France.,Department of Pathology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Violaine Giraud
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Sylvie Labrune
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Jennifer Dumoulin
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Julie Tisserand
- EA4340, Biomarqueursen Cancérologie et Onco-Hématologie, UVSQ, Paris-Saclay University, Boulogne-Billancourt, France.,Department of Pathology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Jean-François Emile
- EA4340, Biomarqueursen Cancérologie et Onco-Hématologie, UVSQ, Paris-Saclay University, Boulogne-Billancourt, France.,Department of Pathology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France
| | - Hélène Blons
- INSERM UMR-S1147, CNRS SNC 5014, Saints-Pères Research Center, 45 rue des Saints-Pères Paris-Descartes University, Sorbonne Paris Cité University, Paris, France.,Department of Molecular Biology, Georges Pompidou European Hospital, 20 rue Leblanc, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Thierry Chinet
- Department of Respiratory Diseases and Thoracic Oncology, APHP - Ambroise Pare Hospital, Boulogne-Billancourt, France.,EA4340, Biomarqueursen Cancérologie et Onco-Hématologie, UVSQ, Paris-Saclay University, Boulogne-Billancourt, France
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69
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Ai B, Liu H, Huang Y, Peng P. Circulating cell-free DNA as a prognostic and predictive biomarker in non-small cell lung cancer. Oncotarget 2018; 7:44583-44595. [PMID: 27323821 PMCID: PMC5190120 DOI: 10.18632/oncotarget.10069] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/29/2016] [Indexed: 01/15/2023] Open
Abstract
Circulating cell-free DNA (cfDNA), which can be obtained from plasma or serum by non-invasive procedures, has showed great potential to predict treatment response and survival for cancer patients. Several studies have assessed the prognostic and predictive value of cfDNA in non-small cell lung cancer (NSCLC). However, these studies were often small and reported varying results. To address this issue, a meta-analysis was carried out. A total of 22 studies involving 2518 patients were subjected to the final analysis. Our results indicated that NSCLC patients with higher cfDNA concentration had shorter median progression-free survival (PFS) and overall survival (OS) time. In addition, high levels of cfDNA were significantly associated with poor PFS (hazard ratio or HR, 1.32; 95% CI, 1.02-1.71) and OS (HR, 1.64; 95% CI, 1.26-2.15). With respect to tumor specific mutations, we failed to reveal significant differences for PFS (HR, 1.30; 95% CI, 0.66-2.56) and OS (HR, 1.05; 95% CI, 0.49-2.25) when NSCLC patients were grouped according to KRAS genotype detected in cfDNA. However, NSCLC patients which harbored EGFR activating mutation in cfDNA had a greater chance of response to EGFR-TKIs (odds ratio or OR, 1.96; 95% CI, 1.59-2.42). No significant publication bias was detected in this study. In conclusion, cfDNA could act as a prognostic and predictive biomarker for patients with NSCLC.
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Affiliation(s)
- Bo Ai
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Huiquan Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Yu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Ping Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
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70
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Yi S, Long F, Cheng J, Huang D. An optimized rapid bisulfite conversion method with high recovery of cell-free DNA. BMC Mol Biol 2017; 18:24. [PMID: 29258436 PMCID: PMC5735811 DOI: 10.1186/s12867-017-0101-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 12/06/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA. RESULTS We optimized a rapid method for the crucial steps of bisulfite conversion with high recovery of cell-free DNA. A rapid deamination step and alkaline desulfonation was combined with the purification of DNA on a silica column. The conversion efficiency and recovery of bisulfite-treated DNA was investigated by the droplet digital PCR. The optimization of the reaction results in complete cytosine conversion in 30 min at 70 °C and about 65% of recovery of bisulfite-treated cell-free DNA, which is higher than current methods. CONCLUSIONS The method allows high recovery from low levels of bisulfite-treated cell-free DNA, enhancing the analysis sensitivity of methylation detection from cell-free DNA.
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Affiliation(s)
- Shaohua Yi
- Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030 China
| | - Fei Long
- Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030 China
| | - Juanbo Cheng
- Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030 China
| | - Daixin Huang
- Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030 China
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71
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Hyun MH, Sung JS, Kang EJ, Choi YJ, Park KH, Shin SW, Lee SY, Kim YH. Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer. Oncotarget 2017; 8:94417-94430. [PMID: 29212238 PMCID: PMC5706884 DOI: 10.18632/oncotarget.21769] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022] Open
Abstract
We used computed tomography (CT) to explore the prognostic value of cell-free (cf) DNA quantification and its predictive efficacy over time after chemotherapy in non-small-cell lung cancer (NSCLC) patients. In total, 177 NSCLC patients were enrolled in a prospective biomarker trial. Consecutive paired blood collection was performed to determine cfDNA concentrations at baseline CT and throughout serial follow-ups. The best cfDNA cut-off value to predict progression-free and overall survival was determined using X-tile analysis. Among 112 chemo-naive patients with stage IV adenocarcinoma, 43 were available for follow-up analysis. Cox regression multivariate analysis indicated that a high cfDNA concentration was an independent negative prognostic factor for progression-free survival (hazard ratio: 2.60; 95% confidence interval: 1.65-4.10; p = 0.008) and overall survival (hazard ratio: 2.63; 95% confidence interval: 1.66-4.17; p < 0.001). However, cfDNA concentration changes during treatment did not correlate with radiological CT responses at first follow-up or best response. No pattern was noted in the percent change in the cfDNA concentration from baseline or subsequently measured level to progression. The serum cfDNA concentration is thus associated with NSCLC patient prognosis, but does not appear to be a clinically valid marker for tumor responses.
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Affiliation(s)
- Myung Han Hyun
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | - Jae Sook Sung
- Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | - Eun Joo Kang
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoon Ji Choi
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyong Hwa Park
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sang Won Shin
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Yong Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yeul Hong Kim
- Division of Medical Oncology, Department of Internal Medicine, Korea University Medical Center, Korea University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Korea University, Seoul, Republic of Korea
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72
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Rostami A, Bratman SV. Utilizing circulating tumour DNA in radiation oncology. Radiother Oncol 2017; 124:357-364. [DOI: 10.1016/j.radonc.2017.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/01/2017] [Accepted: 07/05/2017] [Indexed: 12/25/2022]
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73
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Abstract
Lung cancer is the leading cause of cancer-associated deaths worldwide. Surgery is the standard treatment for early-stage non-small cell lung cancer (NSCLC). Advances in the knowledge of the biology of non-small cell lung cancer have revealed molecular information used for systemic cancer therapy targeting metastatic disease, with an important impact on patients’ overall survival (OS) and quality of life. However, a biopsy of overt metastases is an invasive procedure limited to certain locations and not easily acceptable in the clinic. The analysis of peripheral blood samples of cancer patients represents a new source of cancer-derived material, known as liquid biopsy, and its components (circulating tumour cells (CTCS), circulating free DNA (cfDNA), exosomes, and tumour-educated platelets (TEP)) can be obtained from almost any body fluids. These components have shown to reflect characteristics of the status of both the primary and metastatic diseases, helping the clinicians to move towards a personalized medicine (1). This review focuses on the liquid biopsy component – circulating free DNA, its benefit for non-invasive screening, early diagnosis, prognosis, response to treatment, and real time monitoring of the disease in non-small cell lung cancer patients.
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Affiliation(s)
| | | | - Saulius Cicėnas
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
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74
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Circulating Cell-Free DNA and Circulating Tumor Cells as Prognostic and Predictive Biomarkers in Advanced Non-Small Cell Lung Cancer Patients Treated with First-Line Chemotherapy. Int J Mol Sci 2017; 18:ijms18051035. [PMID: 28492516 PMCID: PMC5454947 DOI: 10.3390/ijms18051035] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022] Open
Abstract
Cell-free DNA (cfDNA) and circulating tumor cells (CTCs) are promising prognostic and predictive biomarkers in non-small cell lung cancer (NSCLC). In this study, we examined the prognostic role of cfDNA and CTCs, in separate and joint analyses, in NSCLC patients receiving first line chemotherapy. Seventy-three patients with advanced NSCLC were enrolled in this study. CfDNA and CTC were analyzed at baseline and after two cycles of chemotherapy. Plasma cfDNA quantification was performed by quantitative PCR (qPCR) whereas CTCs were isolated by the ScreenCell Cyto (ScreenCell, Paris, France) device and enumerated according to malignant features. Patients with baseline cfDNA higher than the median value (96.3 hTERT copy number) had a significantly worse overall survival (OS) and double the risk of death (hazard ratio (HR): 2.14; 95% confidence limits (CL) = 1.24–3.68; p-value = 0.006). Conversely, an inverse relationship between CTC median baseline number (6 CTC/3 mL of blood) and OS was observed. In addition, we found that in patients reporting stable disease (SD), the baseline cfDNA and CTCs were able to discriminate patients at high risk of poor survival. cfDNA demonstrated a more reliable biomarker than CTCs in the overall population. In the subgroup of SD patients, both biomarkers identified patients at high risk of poor prognosis who might deserve additional/alternative therapeutic interventions.
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75
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Chen D, Pan S, Xie E, Gao L, Xu H, Xia W, Xu T, Huang P. Development and Evaluation of a Duplex Real-Time PCR Assay With a Novel Internal Standard for Precise Quantification of Plasma DNA. Ann Lab Med 2017; 37:18-27. [PMID: 27834061 PMCID: PMC5107613 DOI: 10.3343/alm.2017.37.1.18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/25/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Background Circulating levels of cell-free DNA increase in many pathologic conditions. However, notable discrepancies in the quantitative analysis of cell-free DNA from a large number of laboratories have become a considerable pitfall, hampering its clinical application. Methods We designed a novel recombinant DNA fragment that could be applied as an internal standard in a newly developed and validated duplex real-time PCR assay for the quantitative analysis of total cell-free plasma DNA, which was tested in 5,442 healthy adults and 200 trauma patients. Results Compared with two traditional methods, this novel assay showed a lower detection limit of 0.1 ng/mL, lower intra- and inter-assay CVs, and higher accuracy in the recovery test. The median plasma DNA concentration of healthy males (20.3 ng/mL, n=3,092) was significantly higher than that of healthy females (16.1 ng/mL, n=2,350) (Mann-Whitney two-sample rank sum test, P<0.0001). The reference intervals of plasma DNA concentration were 0-45.8 ng/mL and 0-52.5 ng/mL for healthy females and males, respectively. The plasma DNA concentrations of the majority of trauma patients (96%) were higher than the upper normal cutoff values and were closely related to the corresponding injury severity scores (R2=0.916, P<0.0001). Conclusions This duplex real-time PCR assay with a new internal standard could eliminate variation and allow for more sensitive, repeatable, accurate, and stable quantitative measurements of plasma DNA, showing promising application in clinical diagnosis.
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Affiliation(s)
- Dan Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shiyang Pan
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Erfu Xie
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Gao
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huaguo Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenying Xia
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Peijun Huang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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76
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Ansari J, Yun JW, Kompelli AR, Moufarrej YE, Alexander JS, Herrera GA, Shackelford RE. The liquid biopsy in lung cancer. Genes Cancer 2017; 7:355-367. [PMID: 28191282 PMCID: PMC5302037 DOI: 10.18632/genesandcancer.127] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The incidence of lung cancer has significantly increased over the last century, largely due to smoking, and remains the most common cause of cancer deaths worldwide. This is often due to lung cancer first presenting at late stages and a lack of curative therapeutic options at these later stages. Delayed diagnoses, inadequate tumor sampling, and lung cancer misdiagnoses are also not uncommon due to the limitations of the tissue biopsy. Our better understanding of the tumor microenvironment and the systemic actions of tumors, combined with the recent advent of the liquid biopsy, may allow molecular diagnostics to be done on circulating tumor markers, particularly circulating tumor DNA. Multiple liquid biopsy molecular methods are presently being examined to determine their efficacy as surrogates to the tumor tissue biopsy. This review will focus on new liquid biopsy technologies and how they may assist in lung cancer detection, diagnosis, and treatment.
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Affiliation(s)
- Junaid Ansari
- Feist Weiller Cancer Center, LSU Health Shreveport, LA, USA; Department of Molecular and Cellular Physiology, LSU Health Sciences Center, Shreveport, LA, USA
| | - Jungmi W Yun
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center, Shreveport, LA, USA
| | | | | | - Jonathan S Alexander
- Department of Molecular and Cellular Physiology, LSU Health Sciences Center, Shreveport, LA, USA
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77
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Parkinson CA, Gale D, Piskorz AM, Biggs H, Hodgkin C, Addley H, Freeman S, Moyle P, Sala E, Sayal K, Hosking K, Gounaris I, Jimenez-Linan M, Earl HM, Qian W, Rosenfeld N, Brenton JD. Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study. PLoS Med 2016. [PMID: 27997533 DOI: 10.1371/journal.pmed.1002198] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) carrying tumour-specific sequence alterations may provide a minimally invasive means to dynamically assess tumour burden and response to treatment in cancer patients. Somatic TP53 mutations are a defining feature of high-grade serous ovarian carcinoma (HGSOC). We tested whether these mutations could be used as personalised markers to monitor tumour burden and early changes as a predictor of response and time to progression (TTP). METHODS AND FINDINGS We performed a retrospective analysis of serial plasma samples collected during routine clinical visits from 40 patients with HGSOC undergoing heterogeneous standard of care treatment. Patient-specific TP53 assays were developed for 31 unique mutations identified in formalin-fixed paraffin-embedded tumour DNA from these patients. These assays were used to quantify ctDNA in 318 plasma samples using microfluidic digital PCR. The TP53 mutant allele fraction (TP53MAF) was compared to serum CA-125, the current gold-standard response marker for HGSOC in blood, as well as to disease volume on computed tomography scans by volumetric analysis. Changes after one cycle of treatment were compared with TTP. The median TP53MAF prior to treatment in 51 relapsed treatment courses was 8% (interquartile range [IQR] 1.2%-22%) compared to 0.7% (IQR 0.3%-2.0%) for seven untreated newly diagnosed stage IIIC/IV patients. TP53MAF correlated with volumetric measurements (Pearson r = 0.59, p < 0.001), and this correlation improved when patients with ascites were excluded (r = 0.82). The ratio of TP53MAF to volume of disease was higher in relapsed patients (0.04% per cm3) than in untreated patients (0.0008% per cm3, p = 0.004). In nearly all relapsed patients with disease volume > 32 cm3, ctDNA was detected at ≥20 amplifiable copies per millilitre of plasma. In 49 treatment courses for relapsed disease, pre-treatment TP53MAF concentration, but not CA-125, was associated with TTP. Response to chemotherapy was seen earlier with ctDNA, with a median time to nadir of 37 d (IQR 28-54) compared with a median time to nadir of 84 d (IQR 42-116) for CA-125. In 32 relapsed treatment courses evaluable for response after one cycle of chemotherapy, a decrease in TP53MAF of >60% was an independent predictor of TTP in multivariable analysis (hazard ratio 0.22, 95% CI 0.07-0.67, p = 0.008). Conversely, a decrease in TP53MAF of ≤60% was associated with poor response and identified cases with TTP < 6 mo with 71% sensitivity (95% CI 42%-92%) and 88% specificity (95% CI 64%-99%). Specificity was improved when patients with recent drainage of ascites were excluded. Ascites drainage led to a reduction of TP53MAF concentration. The limitations of this study include retrospective design, small sample size, and heterogeneity of treatment within the cohort. CONCLUSIONS In this retrospective study, we demonstrated that ctDNA is correlated with volume of disease at the start of treatment in women with HGSOC and that a decrease of ≤60% in TP53MAF after one cycle of chemotherapy was associated with shorter TTP. These results provide evidence that ctDNA has the potential to be a highly specific early molecular response marker in HGSOC and warrants further investigation in larger cohorts receiving uniform treatment.
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Affiliation(s)
- Christine A Parkinson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Heather Biggs
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Charlotte Hodgkin
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Helen Addley
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Sue Freeman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Penelope Moyle
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Evis Sala
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Karen Sayal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Karen Hosking
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Ioannis Gounaris
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Mercedes Jimenez-Linan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Helena M Earl
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Wendi Qian
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre-Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
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78
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Parkinson CA, Gale D, Piskorz AM, Biggs H, Hodgkin C, Addley H, Freeman S, Moyle P, Sala E, Sayal K, Hosking K, Gounaris I, Jimenez-Linan M, Earl HM, Qian W, Rosenfeld N, Brenton JD. Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study. PLoS Med 2016; 13:e1002198. [PMID: 27997533 PMCID: PMC5172526 DOI: 10.1371/journal.pmed.1002198] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) carrying tumour-specific sequence alterations may provide a minimally invasive means to dynamically assess tumour burden and response to treatment in cancer patients. Somatic TP53 mutations are a defining feature of high-grade serous ovarian carcinoma (HGSOC). We tested whether these mutations could be used as personalised markers to monitor tumour burden and early changes as a predictor of response and time to progression (TTP). METHODS AND FINDINGS We performed a retrospective analysis of serial plasma samples collected during routine clinical visits from 40 patients with HGSOC undergoing heterogeneous standard of care treatment. Patient-specific TP53 assays were developed for 31 unique mutations identified in formalin-fixed paraffin-embedded tumour DNA from these patients. These assays were used to quantify ctDNA in 318 plasma samples using microfluidic digital PCR. The TP53 mutant allele fraction (TP53MAF) was compared to serum CA-125, the current gold-standard response marker for HGSOC in blood, as well as to disease volume on computed tomography scans by volumetric analysis. Changes after one cycle of treatment were compared with TTP. The median TP53MAF prior to treatment in 51 relapsed treatment courses was 8% (interquartile range [IQR] 1.2%-22%) compared to 0.7% (IQR 0.3%-2.0%) for seven untreated newly diagnosed stage IIIC/IV patients. TP53MAF correlated with volumetric measurements (Pearson r = 0.59, p < 0.001), and this correlation improved when patients with ascites were excluded (r = 0.82). The ratio of TP53MAF to volume of disease was higher in relapsed patients (0.04% per cm3) than in untreated patients (0.0008% per cm3, p = 0.004). In nearly all relapsed patients with disease volume > 32 cm3, ctDNA was detected at ≥20 amplifiable copies per millilitre of plasma. In 49 treatment courses for relapsed disease, pre-treatment TP53MAF concentration, but not CA-125, was associated with TTP. Response to chemotherapy was seen earlier with ctDNA, with a median time to nadir of 37 d (IQR 28-54) compared with a median time to nadir of 84 d (IQR 42-116) for CA-125. In 32 relapsed treatment courses evaluable for response after one cycle of chemotherapy, a decrease in TP53MAF of >60% was an independent predictor of TTP in multivariable analysis (hazard ratio 0.22, 95% CI 0.07-0.67, p = 0.008). Conversely, a decrease in TP53MAF of ≤60% was associated with poor response and identified cases with TTP < 6 mo with 71% sensitivity (95% CI 42%-92%) and 88% specificity (95% CI 64%-99%). Specificity was improved when patients with recent drainage of ascites were excluded. Ascites drainage led to a reduction of TP53MAF concentration. The limitations of this study include retrospective design, small sample size, and heterogeneity of treatment within the cohort. CONCLUSIONS In this retrospective study, we demonstrated that ctDNA is correlated with volume of disease at the start of treatment in women with HGSOC and that a decrease of ≤60% in TP53MAF after one cycle of chemotherapy was associated with shorter TTP. These results provide evidence that ctDNA has the potential to be a highly specific early molecular response marker in HGSOC and warrants further investigation in larger cohorts receiving uniform treatment.
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Affiliation(s)
- Christine A. Parkinson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Anna M. Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Heather Biggs
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Charlotte Hodgkin
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Helen Addley
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Sue Freeman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Penelope Moyle
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Evis Sala
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Karen Sayal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Karen Hosking
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Ioannis Gounaris
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Mercedes Jimenez-Linan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Helena M. Earl
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Wendi Qian
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
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79
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Abstract
PURPOSE OF REVIEW This article discusses the current status and applications of liquid biopsy in nonsmall cell lung cancer (NSCLC). RECENT FINDINGS The discovery of genetic alterations which are responsible for the development and progression of NSCLC led to the identification of a new generation of molecular biomarkers. However, in NSCLC, it is often difficult in clinical practice to obtain sufficient tumor material for genetic analyses. Therefore, analyses of tumor-specific genetic alterations in the serum or plasma of the patients are particularly valuable because they can provide temporal measurements of the total tumor burden as well as identify specific mutations that arise during therapy. The procedure of taking blood samples to detect tumor-specific genetic alterations is termed 'liquid biopsy'. In particular, it can be used for a variety of clinical and research applications, including response assessment in epidermal growth factor receptor (EGFR)-mutated NSCLC patients receiving EGFR tyrosine kinase inhibitor therapy. It has been demonstrated that liquid biopsy is a fast and easy way to obtain information on tumor burden and assess the changes of the molecular nature of a tumor during the course of therapy. However, because of the limited amount of tumor material in the blood and yet insufficient knowledge of specific cancer biomarkers, extensive research has to be continued in this field to implement this method into clinical routine. SUMMARY In this review, we highlight the opportunities and clinical as well as research applications of liquid biopsy in NSCLC patients.
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He Y, Zhang X, Wang L, Tian Z, Liu Q, Yao J, Liu Y, Li C, Min L, Shan B. Detection of cancer specific mutations in early-stage non-small cell lung cancer using cell-free DNA by targeted sequencing. Int J Oncol 2016; 49:2351-2358. [DOI: 10.3892/ijo.2016.3731] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/05/2016] [Indexed: 11/06/2022] Open
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Circulating tumor DNA detection in lung cancer patients before and after surgery. Sci Rep 2016; 6:33519. [PMID: 27641744 PMCID: PMC5027588 DOI: 10.1038/srep33519] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/30/2016] [Indexed: 12/18/2022] Open
Abstract
Circulating tumor DNA (ctDNA) in peripheral blood is a "liquid biopsy" that contains representative tumor information including gene mutations. Additionally, repeated ctDNA samples can be easily obtained to monitor response to treatment and disease progression, which may be especially valuable to lung cancer patients with tumors that cannot be easily biopsied or removed. To investigate the changes in ctDNA after surgical tumor resection, tumor and blood samples obtained before and after surgery were collected prospectively from 41 non-small lung cancer (NSCLC) patients. Somatic driver mutations in tumor DNA (tDNA) and pre- and post-op plasma ctDNA sample pairs were identified by targeted sequencing in several genes including EGFR, KRAS, and TP53 with an overall study concordance of 78.1% and sensitivity and specificity of 69.2% and 93.3%, respectively. Importantly, the frequency of 91.7% of ctDNA mutations decreased after surgery and these changes were observed as little as 2 days post-op. Moreover, the presence of ctDNA had a higher positive predictive value than that of six tumor biomarkers in current clinical use. This study demonstrates the use of targeted sequencing to reliably identify ctDNA changes in response to treatment, indicating a potential utility of this approach in the clinical management of NSCLC.
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Circulating Tumor DNA Detection in Early-Stage Non-Small Cell Lung Cancer Patients by Targeted Sequencing. Sci Rep 2016; 6:31985. [PMID: 27555497 PMCID: PMC4995492 DOI: 10.1038/srep31985] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) isolated from peripheral blood has recently been shown to be an alternative source to detect gene mutations in primary tumors; however, most previous studies have focused on advanced stage cancers, and few have evaluated ctDNA detection in early-stage lung cancer. In the present study, blood and tumor samples were collected prospectively from 58 early-stage non-small lung cancer (NSCLC) patients (stages IA, IB, and IIA) and a targeted sequencing approach was used to detect somatic driver mutations in matched tumor DNA (tDNA) and plasma ctDNA. We identified frequent driver mutations in plasma ctDNA and tDNA in EGFR, KRAS, PIK3CA, and TP53, and less frequent mutations in other genes, with an overall study concordance of 50.4% and sensitivity and specificity of 53.8% and 47.3%, respectively. Cell-free (cfDNA) concentrations were found to be significantly associated with some clinical features, including tumor stage and subtype. Importantly, the presence of cfDNA had a higher positive predictive value than that of currently used protein tumor biomarkers. This study demonstrates the feasibility of identifying plasma ctDNA mutations in the earliest stage lung cancer patients via targeted sequencing, demonstrating a potential utility of targeted sequencing of ctDNA in the clinical management of NSCLC.
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Pathologists and liquid biopsies: to be or not to be? Virchows Arch 2016; 469:601-609. [PMID: 27553354 DOI: 10.1007/s00428-016-2004-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/25/2016] [Accepted: 08/09/2016] [Indexed: 12/19/2022]
Abstract
Recently, the advent of therapies targeting genomic alterations has improved the care of patients with certain types of cancer. While molecular targets were initially detected in nucleic acid samples extracted from tumor tissue, detection of nucleic acids in circulating blood has allowed the development of what has become known as liquid biopsies, which provide a complementary and alternative sample source allowing identification of genomic alterations that might be addressed by targeted therapy. Consequently, liquid biopsies might rapidly revolutionize oncology practice in allowing administration of more effective treatments. Liquid biopsies also provide an approach towards short-term monitoring of metastatic cancer patients to evaluate efficacy of treatment and/or early detection of secondary mutations responsible for resistance to treatment. In this context, pathologists, who have already been required in recent years to take interest in the domain of molecular pathology of cancer, now face new challenges. The attitude of pathologists to and level of involvement in the practice of liquid biopsies, including mastering the methods employed in molecular analysis of blood samples, need close attention. Regardless of the level of involvement of pathologists in this new field, it is mandatory that oncologists, biologists, geneticists, and pathologists work together to coordinate the pre-analytical, analytical, and post-analytical phases of molecular assessment of tissue and liquid samples of individual cancer patients. The challenges include (1) implementation of effective and efficient procedures for reception and analysis of liquid and tissue samples for histopathological and molecular evaluation and (2) assuring short turn-around times to facilitate rapid optimization of individual patient treatment. In this paper, we will review the following: (1) recent data concerning the concept of liquid biopsies in oncology and its development for patient care, (2) advantages and limitations of molecular analyses performed on blood samples compared to those performed on tissue samples, and (3) short-term challenges facing pathologists in dealing with liquid biopsies of cancer patients and new strategies to early detect metastatic tumor cell clones.
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Cargnin S, Canonico PL, Genazzani AA, Terrazzino S. Quantitative Analysis of Circulating Cell-Free DNA for Correlation with Lung Cancer Survival: A Systematic Review and Meta-Analysis. J Thorac Oncol 2016; 12:43-53. [PMID: 27543256 DOI: 10.1016/j.jtho.2016.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/20/2016] [Accepted: 08/02/2016] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the growing interest in circulating cell-free DNA (cfDNA), no conclusive evidence exists on the value of quantitative analysis of cfDNA for the prediction of lung cancer survival. We performed a systematic review and meta-analysis of primary studies to estimate the impact of higher baseline cfDNA levels on survival outcomes of patients with lung cancer. METHODS A comprehensive search was performed using the PubMed, Web of Knowledge, and Cochrane databases up to March 2016. The methodologic quality of identified studies was assessed by the Newcastle-Ottawa scale. Potential sources of heterogeneity were investigated via subgroup and sensitivity analyses, while publication bias was evaluated by funnel plot and Egger's test. RESULTS Among the 17 studies identified, 16 studies (n = 1723 patients) and 5 studies (n = 640) were included in the meta-analysis of overall survival (OS) and progression-free survival (PFS), respectively. Despite the fact that the association with PFS did not reach statistical significance (hazard ratio 1.12% [95% confidence interval 0.91-1.37), the pooled analysis for OS showed evidence of an increased risk of death in patients with higher baseline cfDNA levels (hazard ratio 1.76 [95% confidence interval 1.38-2.25]; p < 0.001). Further subgroup and sensitivity analyses confirmed this relationship, although significant between-study heterogeneity was still detected in most comparisons. The Egger's test revealed no statistical evidence of publication bias in the results. CONCLUSION Our findings support the clinical validity of quantitative analysis of cfDNA for the prediction of lung cancer survival. Nevertheless, the establishment of a robust standardized method for determination of optimal cutoff thresholds is required to define the clinical relevance of cfDNA quantification for lung cancer management.
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Affiliation(s)
- Sarah Cargnin
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics, University of Piemonte Orientale "A. Avogadro," Novara, Italy
| | - Pier Luigi Canonico
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics, University of Piemonte Orientale "A. Avogadro," Novara, Italy
| | - Armando A Genazzani
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics, University of Piemonte Orientale "A. Avogadro," Novara, Italy
| | - Salvatore Terrazzino
- Department of Pharmaceutical Sciences and Interdepartmental Research Center of Pharmacogenetics and Pharmacogenomics, University of Piemonte Orientale "A. Avogadro," Novara, Italy.
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Izumo T, Matsumoto Y, Chavez C, Tsuchida T. Re-biopsy by endobronchial ultrasound procedures for mutation analysis of non-small cell lung cancer after EGFR tyrosine kinase inhibitor treatment. BMC Pulm Med 2016; 16:106. [PMID: 27457475 PMCID: PMC4960795 DOI: 10.1186/s12890-016-0268-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/19/2016] [Indexed: 12/24/2022] Open
Abstract
Background Re-biopsy for resistant non-small cell lung cancer (NSCLC) after treatment with epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) is important for selection of better therapy, but there have been no reports about the utility of endobronchial ultrasound (EBUS)-guided procedures for such purpose. The aim of this study was to evaluate the utility of EBUS-guided re-biopsy for resistant NSCLC after treatment with EGFR-TKIs. Methods From January 2013 to December 2015, 53 consecutive patients who underwent EBUS-guided re-biopsy for mutation analysis of NSCLC after EGFR-TKI treatment were assessed. Results Nine patients underwent EBUS-guided transbronchial needle aspiration (EBUS-TBNA) and 44 patients underwent EBUS with a guide sheath (EBUS-GS) transbronchial biopsy. The technical success rates were 100 %. As for mutation analysis, all 9 specimens (100 %) from EBUS-TBNA and 33 specimens (75.0 %) from EBUS-GS were adequate for gene profiling. The remaining 11 specimens from EBUS-GS procedures were inadequate for mutation analysis owing to the absence of tumor component in the sample (n = 6) or insufficient specimen (n = 5). There were no related severe complications. Conclusions Re-biopsy by both EBUS-TBNA and EBUS-GS were useful and safe sampling procedures for mutation analysis of EGFR-TKI resistant NSCLC.
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Affiliation(s)
- Takehiro Izumo
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, 5-1-1, Tsukiji Chou-ku, Tokyo, 104-0045, Japan.
| | - Yuji Matsumoto
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, 5-1-1, Tsukiji Chou-ku, Tokyo, 104-0045, Japan
| | - Christine Chavez
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, 5-1-1, Tsukiji Chou-ku, Tokyo, 104-0045, Japan
| | - Takaaki Tsuchida
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, 5-1-1, Tsukiji Chou-ku, Tokyo, 104-0045, Japan
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Li T, Zheng Y, Sun H, Zhuang R, Liu J, Liu T, Cai W. K-Ras mutation detection in liquid biopsy and tumor tissue as prognostic biomarker in patients with pancreatic cancer: a systematic review with meta-analysis. Med Oncol 2016; 33:61. [PMID: 27225938 DOI: 10.1007/s12032-016-0777-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/14/2016] [Indexed: 01/06/2023]
Abstract
K-Ras gene mutations have been found in most pancreatic cancers; however, conflicting data on the prognostic value of K-Ras mutations in pancreatic cancer have been published. We conducted a meta-analysis to assess its prognostic significance. Literature searches of PubMed, EMBASE, Cochrane Library, Web of Science and Google Scholar were performed through December 2015 to identify publications exploring the association of K-Ras mutation with overall survival. Forty eligible studies involving 3427 patients with pancreatic cancer were included in the present meta-analysis. Our analysis showed a hazard ratio (HR) of negative association with survival of 1.61 [95 % confidence interval (CI) 1.36-1.90; p < 0.01] in K-Ras mutant pancreatic cancer patients. In subgroup analyses, K-Ras mutations detected in tumor tissues and in liquid biopsies had HRs of 1.37 (95 % CI 1.20-1.57; p < 0.01) and 3.16 (95 % CI 2.1-4.71; p < 0.01), respectively. In addition, the HR was higher when K-Ras mutations were detected in fresh frozen samples (HR = 2.01, 95 % CI 1.28-3.16, p = 0.002) than in formalin-fixed, paraffin-embedded (FFPE) samples (HR = 1.29, 95 % CI 1.12-1.49, p < 0.01). Though K-Ras alterations are more frequent among non-East Asian individuals than East Asian individuals, there were no significant differences in HRs of survival between the two ethnic subgroups. In conclusion, this meta-analysis suggests that K-Ras mutations are associated with a worse overall survival in pancreatic cancer patients, especially when mutations are detected in liquid biopsies or fresh frozen tumor tissue samples.
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Affiliation(s)
- Tao Li
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Yuanting Zheng
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Hong Sun
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Rongyuan Zhuang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Liu
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weimin Cai
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China.
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Wei Z, Shah N, Deng C, Xiao X, Zhong T, Li X. Circulating DNA addresses cancer monitoring in non small cell lung cancer patients for detection and capturing the dynamic changes of the disease. SPRINGERPLUS 2016; 5:531. [PMID: 27186495 PMCID: PMC4844578 DOI: 10.1186/s40064-016-2141-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/12/2016] [Indexed: 11/18/2022]
Abstract
Purpose Monitoring of key markers for lung cancer detection and tracking of acquired drug resistance is critical for the management of the disease. We aim to ascertain the value of monitoring both total cell free DNA concentrations and mutant EGFR DNA content within diverse groups of individuals most vulnerable to the disease. Methods We proposed longitudinal monitoring of circulating DNA using digital PCR. Circulating DNA present in peripheral blood can be obtained non-invasively and provide timely disease status update. 25 heavy smokers and 50 patients undergoing TKI therapy were recruited. Peripheral blood specimens were taken at different time points and their circulating DNA were analyzed and quantified. Results Significant higher concentrations of total cell free DNA were detected when compared with healthy high-risk individuals. Levels were stable throughout the treatment cycles, which makes it potentially a useful tool for patient stratification. Concurrent mutant T790M DNA detection of lung cancer patients at baseline achieved 82 % concordance with matched tissue analysis. Samples initially negative for the T790M gene mutation that became positive during treatment were corroborated with a repeat biopsy. The results showed its usefulness for serial monitoring. Conclusion Monitoring of circulating DNA addresses the need for disease detection and shows the ability to capture the dynamic changes of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2141-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhangjing Wei
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Nirej Shah
- Department of Clinical Medicine, JingChu University of Technology, JingMen, People's Republic of China
| | - Chong Deng
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Xuehui Xiao
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Tenglang Zhong
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Xiansong Li
- Department of Neurosurgery, JingZhou Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Renmin Road 1, JingZhou, 434020 People's Republic of China
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Jung M, Pützer S, Gevensleben H, Meller S, Kristiansen G, Dietrich D. Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant, and malignant ascites. Clin Epigenetics 2016; 8:24. [PMID: 26937257 PMCID: PMC4774089 DOI: 10.1186/s13148-016-0192-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cytology remains the gold standard for the detection of malignant cells in ascites. However, its sensitivity is limited. The aim of this study was to evaluate DNA methylation biomarkers for the differential diagnosis of benign (ascites in patients without malignancy), malignant (ascites in cancer patients directly caused by malignancy), and paramalignant (ascites in cancer patients caused by comorbidities but not by malignancy) ascites. METHODS A cohort of 283 patients (134 cancer patients, 149 patients with benign diseases) presenting with ascites was prospectively enrolled. Ascites was evaluated by means of cytopathological investigation and DNA methylation of SHOX2 and SEPT9 in the cell-free and cellular fraction. DNA methylation in bisulfite-converted DNA was determined using quantitative methylation specific real-time PCR. Cytopathological and DNA methylation results were evaluated with regard to diagnosis and overall survival (OS). RESULTS Patients with positive DNA methylation had a poor overall survival compared to methylation-negative patients (hazard ratio: HR = 1.97, p = 0.001). In multivariate survival analysis, DNA methylation was an independent prognostic parameter (p = 0.003) together with age (HR = 1.03, p < 0.001) and the presence of malignant disease (HR = 1.87, p < 0.001). The combination of methylation with cytopathological analyses led to a 42 % increase in the detection rate of malignant ascites, resulting in 37 % positively diagnosed cancer patients and a specificity of 97 %. Among cancer patients, patients with DNA methylation-positive ascites showed an adverse clinical course (HR = 1.63, p = 0.039). CONCLUSIONS DNA methylation testing adds diagnostic and prognostic information and might constitute an effective ancillary method for the differential diagnosis of malignant, paramalignant, and benign ascites.
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Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Svenja Pützer
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Heidrun Gevensleben
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Sebastian Meller
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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El Messaoudi S, Mouliere F, Du Manoir S, Bascoul-Mollevi C, Gillet B, Nouaille M, Fiess C, Crapez E, Bibeau F, Theillet C, Mazard T, Pezet D, Mathonnet M, Ychou M, Thierry AR. Circulating DNA as a Strong Multimarker Prognostic Tool for Metastatic Colorectal Cancer Patient Management Care. Clin Cancer Res 2016; 22:3067-77. [DOI: 10.1158/1078-0432.ccr-15-0297] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 01/03/2016] [Indexed: 02/07/2023]
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90
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Remon J, Gorham J, Besse B, Sculier JP. Circulating free DNA, new dynamic marker in nonsmall cell lung cancer patients? Eur Respir J 2015; 46:1548-50. [DOI: 10.1183/13993003.01482-2015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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