1
|
Verlicchi A, Canale M, Chiadini E, Cravero P, Urbini M, Andrikou K, Pasini L, Flospergher M, Burgio MA, Crinò L, Ulivi P, Delmonte A. The Clinical Significance of Circulating Tumor DNA for Minimal Residual Disease Identification in Early-Stage Non-Small Cell Lung Cancer. Life (Basel) 2023; 13:1915. [PMID: 37763318 PMCID: PMC10532754 DOI: 10.3390/life13091915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/18/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Lung cancer (LC) is the deadliest malignancy worldwide. In an operable stage I-III patient setting, the detection of minimal residual disease (MRD) after curative treatment could identify patients at higher risk of relapse. In this context, the study of circulating tumor DNA (ctDNA) is emerging as a useful tool to identify patients who could benefit from an adjuvant treatment, and patients who could avoid adverse events related to a more aggressive clinical management. On the other hand, ctDNA profiling presents technical, biological and standardization challenges before entering clinical practice as a decisional tool. In this paper, we review the latest advances regarding the role of ctDNA in identifying MRD and in predicting patients' prognosis, with a particular focus on clinical trials investigating the potential of ctDNA, the technical challenges to address and the biological parameters that influence the MRD detection.
Collapse
Affiliation(s)
- Alberto Verlicchi
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Paola Cravero
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Kalliopi Andrikou
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Luigi Pasini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Michele Flospergher
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Marco Angelo Burgio
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Angelo Delmonte
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| |
Collapse
|
2
|
Crintea A, Constantin AM, Motofelea AC, Crivii CB, Velescu MA, Coșeriu RL, Ilyés T, Crăciun AM, Silaghi CN. Targeted EGFR Nanotherapy in Non-Small Cell Lung Cancer. J Funct Biomater 2023; 14:466. [PMID: 37754880 PMCID: PMC10532491 DOI: 10.3390/jfb14090466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide. Despite advances in treatment, the prognosis remains poor, highlighting the need for novel therapeutic strategies. The present review explores the potential of targeted epidermal growth factor receptor (EGFR) nanotherapy as an alternative treatment for NSCLC, showing that EGFR-targeted nanoparticles are efficiently taken up by NSCLC cells, leading to a significant reduction in tumor growth in mouse models. Consequently, we suggest that targeted EGFR nanotherapy could be an innovative treatment strategy for NSCLC; however, further studies are needed to optimize the nanoparticles and evaluate their safety and efficacy in clinical settings and human trials.
Collapse
Affiliation(s)
- Andreea Crintea
- Department of Molecular Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.C.); (T.I.); (C.N.S.)
| | - Anne-Marie Constantin
- Department of Morphological Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.-M.C.); (C.-B.C.)
| | - Alexandru C. Motofelea
- Department of Internal Medicine, University of Medicine and Pharmacy “Victor Babeș”, 300041 Timișoara, Romania;
| | - Carmen-Bianca Crivii
- Department of Morphological Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.-M.C.); (C.-B.C.)
| | - Maria A. Velescu
- Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania;
| | - Răzvan L. Coșeriu
- Department of Microbiology, University of Medicine, Pharmacy, Science and Technology “George Emil Palade”, 540142 Târgu-Mureș, Romania;
| | - Tamás Ilyés
- Department of Molecular Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.C.); (T.I.); (C.N.S.)
| | - Alexandra M. Crăciun
- Department of Molecular Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.C.); (T.I.); (C.N.S.)
| | - Ciprian N. Silaghi
- Department of Molecular Sciences, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400349 Cluj-Napoca, Romania; (A.C.); (T.I.); (C.N.S.)
| |
Collapse
|
3
|
Yu Q, Jiang H, Su X, Jiang Z, Liang X, Zhang C, Shang W, Zhang Y, Chen H, Yang Z, Shen M, Huang F, Chen X, Yang Y, Pan B, Wang B, Lu D, Guo W. Development of multiplex drop-off digital PCR assays for hotspot mutation detection of KRAS, NRAS, BRAF and PIK3CA in the plasma of colorectal cancer patients. J Mol Diagn 2023; 25:388-402. [PMID: 36963484 DOI: 10.1016/j.jmoldx.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The detection of mutations in KRAS, NRAS, BRAF and PIK3CA has become essential in treatment management of metastatic colorectal cancer (mCRC), with the approval of new targeted therapies. We developed novel multiplex drop-off digital PCR (MDO-dPCR) assays, by combining amplitude-/ratio-based multiplexing with drop-off/double drop-off strategies, which allow for detection of at least 69 most frequent hotspot mutations in all four genes with only three reactions. We assessed the analytical performance of the assays using synthetic oligonucleotides, further validated on plasma cfDNA samples from a large cohort of CRC patients and compared with next generation sequencing (NGS) data. The MDO-dPCR assays showed a high sensitivity with a limit of detection (LOD) ranging from 0.084 to 0.182% in mutant allelic frequency (MAF). The screening of plasma cfDNAs from 106 CRC patients identified mutations in 42.45% of them, with a sensitivity of 95.24%, a specificity of 98.53% and an accuracy of 96.98% for mutation detection and a strong correlation of measured MAFs as compared to NGS results. The high sensitivity and comprehensive mutation coverage of the MDO-dPCR assays make them suitable for rapid and cost-effective detection of KRAS, NRAS, BRAF and PIK3CA mutations in the plasma of CRC patients, and could be useful in early response assessment and longitudinal disease monitoring.
Collapse
Affiliation(s)
- Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Huiqin Jiang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Su
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Xue Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Wu Shang
- Nanjing Pregene Biotechnology, Nanjing, China
| | | | - Hao Chen
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Zhijie Yang
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinning Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihui Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
| |
Collapse
|
4
|
Slonim LB, Mangold KA, Alikhan MB, Joseph N, Reddy KS, Sabatini LM, Kaul KL. Cell-free Nucleic Acids in Cancer: Current Approaches, Challenges, and Future Directions. Clin Lab Med 2022; 42:669-686. [PMID: 36368789 DOI: 10.1016/j.cll.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liron Barnea Slonim
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kathy A Mangold
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Mir B Alikhan
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Nora Joseph
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kalpana S Reddy
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Linda M Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Karen L Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201.
| |
Collapse
|
5
|
Challenges in promoter methylation analysis in the new era of translational oncology: a focus on liquid biopsy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166390. [PMID: 35296416 DOI: 10.1016/j.bbadis.2022.166390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Toward the discovery of novel reliable biomarkers, epigenetic alterations have been repeatedly proposed for the diagnosis and the development of therapeutic strategies against cancer. Indeed, for promoter methylation to actively become a tumor marker for clinical use, it must be combined with a highly informative technology evaluated in an appropriate biospecimen. Methodological standardization related to epigenetic research is, in fact, one of the most challenging tasks. Moreover, tissue-based biopsy is being complemented and, in some cases, replaced by liquid biopsy. This review will highlight the advancements made for both pre-analytical and analytical implementation for the prospective use of methylation biomarkers in clinical settings, with particular emphasis on liquid biopsy.
Collapse
|
6
|
Validation of a One-Step Reverse Transcription-Droplet Digital PCR (RT-ddPCR) Approach to Detect and Quantify SARS-CoV-2 RNA in Nasopharyngeal Swabs. DISEASE MARKERS 2021; 2021:8890221. [PMID: 33747257 PMCID: PMC7934789 DOI: 10.1155/2021/8890221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/15/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. Quantitative reverse transcription-PCR (RT-qPCR) is, to this day, the preferred methodology for viral RNA detection, even if not without problems. To overcome some of the limitations still existing for the detection and quantification of nucleic acids in various applications, the use of one-step reverse transcription-droplet digital PCR (RT-ddPCR) has been established. The purpose of this study was, then, to evaluate the efficacy of ddPCR for the detection of SARS-CoV-2 RNA in nasopharyngeal swabs, optimizing the detection of low-viral load-burdened samples. Methods The RT-ddPCR workflow was validated for sensitivity, specificity, linearity, reproducibility, and precision using samples from 90 COVID-19-infected patients referred to the Department of Laboratory Medicine of the University Hospital of Udine (Italy). Results The present study shows that RT-ddPCR allows the detection of as low as 10.3 copies of a SARS-COV-2 E-gene per sample with a higher level of accuracy and precision, especially at low concentration. Conclusion During the postpeak phase of the SARS-CoV-2 pandemic, it is essential to rely on a highly robust molecular biology method to identify infected subjects, whether they have symptoms or not, in order to prepare appropriate containment measures.
Collapse
|
7
|
Plasma-based early screening and monitoring of EGFR mutations in NSCLC patients by a 3-color digital PCR assay. Br J Cancer 2020; 123:1437-1444. [PMID: 32782293 PMCID: PMC7592053 DOI: 10.1038/s41416-020-1024-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/30/2022] Open
Abstract
Background Noninvasive plasma-based detection of EGFR mutations using digital PCR promises a fast, sensitive and reliable approach to predicting the efficiency of EGFR-TKI. However, the low throughput and high cost of digital PCR restricts its clinical application. Methods We designed a digital PCR assay, which can simultaneously detect 39 mutations of exons 18–21 of the EGFR gene. To assess overall performance, retrospective FFPE tissues from 30 NSCLC patients and plasma from 33 NSCLC patients were collected and analysed. Results The LoD of the EGFR mutations was as low as 0.308 copies/μL, and the linear correlation between the detected and expected values at different concentrations (0.01–10%) was low as well. Compared to ARMS-PCR in FFPE, the accuracy values of the dEGFR39 assay in plasma from 33 patients was 87.88% (29/33, 95% CI 72.67–95.18%). While monitoring the 33 patients, the EGFR mutation load as assessed by dEGFR39 was associated with the objective response to treatment. Thirteen samples from eight patients were identified by dEGFR39 to harbour the T790M mutation over time; of these patients, only nine (69%) were detected using SuperARMS. Conclusion Our results indicate that dEGFR39 assay is reliable, sensitive and cost-efficient. This method is beneficial for profiling EGFR mutations for precision therapy and prognosis after TKI treatment, especially in patients with insufficient tissue biopsy samples.
Collapse
|
8
|
Yang Z, Li J, Hu Y, Chen M, Peng D, Zong D, Shang Q, Tao L, Zhao Y, Ni Y, Ye J, Xie Y, Yang L, Lin Q, Cai C, Xu N, Huang X, Dong X, Zhou Z, Yu Y, Shangguan Z, Xu Y, Ying W, Weng M, Yuan Z, Dong Z, Li J, Zheng Z, Pan J, Liu L, Ye J, Zhang Z, Li W, Zhu J, Jin S, Li Y, Ding C. Dynamics of Plasma EGFR T790M Mutation in Advanced NSCLC: A Multicenter Study. Target Oncol 2020; 14:719-728. [PMID: 31691892 DOI: 10.1007/s11523-019-00682-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Droplet digital polymerase chain reaction (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, a ddPCR assay for the epidermal growth factor receptor (EGFR) p.Thr790Met (T790M) mutation suitable for clinical use remains to be established with analytical and clinical validations. OBJECTIVE We aimed to develop and validate a new ddPCR assay to quantify the T790M mutation in plasma for monitoring and predicting the progression of advanced non-small-cell lung cancer (NSCLC). METHODS Specificity of the ddPCR assay was evaluated with genomic DNA samples from healthy individuals. The inter- and intraday variations of the assay were evaluated using mixtures of plasmid DNA containing wild-type EGFR and T790M mutation sequences. We assessed the clinical utility of the T790M assay in a multicenter prospective study in patients with advanced NSCLC receiving tyrosine kinase inhibitor (TKI) treatment by analyzing longitudinal plasma DNA samples. RESULTS We set the criteria for a positive call when the following conditions were satisfied: (1) T790M mutation frequency > 0.098% (3 standard deviations above the background signal); (2) at least two positive droplets in duplicate ddPCR reactions. Among the 62 patients with advanced NSCLC exhibiting resistance to TKI treatment, 15 had one or more serial plasma samples that tested positive for T790M. T790M mutation was detected in the plasma as early as 205 days (median 95 days) before disease progression, determined by imaging analysis. Plasma T790M concentrations also correlated with intervention after disease progression. CONCLUSIONS We developed a ddPCR assay to quantify the T790M mutation in plasma. Quantification of longitudinal plasma T790M mutation may allow noninvasive assessment of drug resistance and guide follow-up treatment in TKI-treated patients with NSCLC. TRIAL REGISTRATION Clinical Trials.gov identifier: NCT02804100.
Collapse
Affiliation(s)
- Zhengquan Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jialu Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yujie Hu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meihua Chen
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Danli Peng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dan Zong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingjuan Shang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lianqin Tao
- Department of Pulmonary Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Yanling Zhao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiyun Ni
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinyan Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yupeng Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Li Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Quan Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chang Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ning Xu
- Department of Respiratory Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Xiaoping Huang
- Department of Respiratory Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Xiaoting Dong
- Wenzhou Hospital of Traditional Chinese Medicine, Wenzhou, Zhejiang, China
| | - Zhonghui Zhou
- Ningbo Hospital of Traditional Chinese Medicine, Ningbo, Zhejiang, China
| | - Yali Yu
- Ningbo Hospital of Traditional Chinese Medicine, Ningbo, Zhejiang, China
| | - Zongxiao Shangguan
- The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yangyang Xu
- Zhejiang Jinhua Guangfu Hospital, Jinhua, Zhejiang, China
| | - Weiping Ying
- Zhejiang Jinhua Guangfu Hospital, Jinhua, Zhejiang, China
| | - Meiling Weng
- Department of Oncology, The People's Hospital of Quzhou, Quzhou, Zhejiang, China
| | - Zuguo Yuan
- Department of Radiotherapy and Chemotherapy, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Zhijun Dong
- ChinacoHealthcare Corporation International Hospital, Ningbo, Zhejiang, China
| | - Jifa Li
- Yue Qing General Hospital, Yue Qing, Zhejiang, China
| | - Zhe Zheng
- The Ping Yang Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiongwei Pan
- Department of Respiratory and Critical Care Medicine, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Lu Liu
- Department of Interventional Radiology, Zhejiang University Lishui Hospital, Lishui, Zhejiang, China
| | - Junhui Ye
- Department of Respiratory Medicine, Sanmen People's Hospital of Zhejiang, Taizhou, Zhejiang, China
| | - Zhan Zhang
- Huangyan Hospital of Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Wenfeng Li
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junfei Zhu
- Department of Pulmonary Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China.
| | - Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| |
Collapse
|
9
|
Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A. ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA. Bioinformatics 2020; 36:2665-2674. [PMID: 31922552 PMCID: PMC7203757 DOI: 10.1093/bioinformatics/btaa016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/04/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. RESULTS We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. AVAILABILITY AND IMPLEMENTATION ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus, and it is also available at CRAN official R repository. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Nicola Casiraghi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Francesco Orlando
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Jenny Xiang
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Genomics and Epigenomics Core Facility
| | - Andrea Sboner
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gerhardt Attard
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| |
Collapse
|
10
|
The Validity and Predictive Value of Blood-Based Biomarkers in Prediction of Response in the Treatment of Metastatic Non-Small Cell Lung Cancer: A Systematic Review. Cancers (Basel) 2020; 12:cancers12051120. [PMID: 32365836 PMCID: PMC7280996 DOI: 10.3390/cancers12051120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
With the introduction of targeted therapies and immunotherapy, molecular diagnostics gained a more profound role in the management of non-small cell lung cancer (NSCLC). This study aimed to systematically search for studies reporting on the use of liquid biopsies (LB), the correlation between LBs and tissue biopsies, and finally the predictive value in the management of NSCLC. A systematic literature search was performed, including results published after 1 January 2014. Articles studying the predictive value or validity of a LB were included. The search (up to 1 September 2019) retrieved 1704 articles, 1323 articles were excluded after title and abstract screening. Remaining articles were assessed for eligibility by full-text review. After full-text review, 64 articles investigating the predictive value and 78 articles describing the validity were included. The majority of studies investigated the predictive value of LBs in relation to therapies targeting the epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) receptor (n = 38). Of studies describing the validity of a biomarker, 55 articles report on one or more EGFR mutations. Although a variety of blood-based biomarkers are currently under investigation, most studies evaluated the validity of LBs to determine EGFR mutation status and the subsequent targeting of EGFR tyrosine kinase inhibitors based on the mutation status found in LBs of NSCLC patients.
Collapse
|
11
|
Li C, He Q, Liang H, Cheng B, Li J, Xiong S, Zhao Y, Guo M, Liu Z, He J, Liang W. Diagnostic Accuracy of Droplet Digital PCR and Amplification Refractory Mutation System PCR for Detecting EGFR Mutation in Cell-Free DNA of Lung Cancer: A Meta-Analysis. Front Oncol 2020; 10:290. [PMID: 32195189 PMCID: PMC7063461 DOI: 10.3389/fonc.2020.00290] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Epidermal growth factor receptor (EGFR) mutation testing in plasma cell-free DNA (cfDNA) from advanced lung cancer patients is an emerging clinical tool. This meta-analysis was designed to determine the diagnostic accuracy of two common PCR systems, droplet digital PCR (ddPCR) and amplification refractory mutation system PCR (ARMS-PCR), for detecting EGFR mutation in cfDNA. Materials and methods: A systematic search was carried out based on PubMed, Web of science, Embase and the Cochrane library. Data from eligible studies were extracted and pooled to calculate the sensitivity, specificity, diagnostic odds ratio (DOR), area under the summary receiver-operating characteristic curve (AUROC), using tissue biopsy results as the standard method. Subgroup analyses were performed regarding EGFR mutation type, tumor stage, and EGFR-TKI treatment. Results: Twenty-five studies involving 4,881 cases were included. The plasma testing sensitivity, specificity, DOR, and AUROC, compared with the matched tumor tissues, were 72.1%, 95.6%, 38.5, 0.89 for ddPCR, and 65.3%, 98.2%, 52.8, 0.71 for ARMS-PCR, respectively, through indirect comparison, significant differences were found in sensitivity (P = 0.003) and specificity (P = 0.007). Furthermore, significant difference was found in sensitivity between tumor stage subgroups (IIIB–IV subgroup vs. IA–IV subgroup) in ARMS-PCR (73.7 vs. 64.2%, P = 0.008), but not in ddPCR (72.5 vs. 71.2%, P = 0.756). Conclusions: This study demonstrates that ddPCR and ARMS-PCR have a high specificity with a practical sensitivity for detecting EGFR mutation in cfDNA, which supports their application as a supplement or a conditional-alternative to tissue biopsy in clinical practice for genotyping. It seems that ddPCR has a higher sensitivity than ARMS-PCR, especially in early stages.
Collapse
Affiliation(s)
- Caichen Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qihua He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hengrui Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Cheng
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianfu Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Xiong
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yi Zhao
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Minzhang Guo
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhichao Liu
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhua Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
12
|
Abstract
ctDNA provided by liquid biopsy offers a promising alternative to tumor biopsy as it gives a non-invasive and «real-time» access to the cancer genome and reflects tumor intra and extra heterogeneity. ctDNA has shown growing clinical interest for cancer diagnosis, prognosis, theragnostics, therapeutic monitoring, and clonal evolution tracking. A major technical limit for ctDNA analysis from body fluids is the extremely low proportion of ctDNA compared to non-malignant cell-free DNA, underscoring the need for highly sensitive and specific detection techniques. The control of pre-analytical procedures appears essential for optimal ctDNA analysis and need to be standardized for clinical research applications. This chapter provides insights into major current technologies for ctDNA detection. Overall, PCR-based techniques are able to detect limited molecular alterations and have a high sensitivity suitable for monitoring purposes while NGS-based approaches are broad range molecular screening assays more specifically indicated for treatment selection. We briefly reviewed new technical innovations that are now available for ctDNA detection.
Collapse
Affiliation(s)
- Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000, Nancy, France.
| |
Collapse
|
13
|
Jahangiri L, Hurst T. Assessing the Concordance of Genomic Alterations between Circulating-Free DNA and Tumour Tissue in Cancer Patients. Cancers (Basel) 2019; 11:cancers11121938. [PMID: 31817150 PMCID: PMC6966532 DOI: 10.3390/cancers11121938] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Somatic alterations to the genomes of solid tumours, which in some cases represent actionable drivers, provide diagnostic and prognostic insight into these complex diseases. Spatial and longitudinal tracking of somatic genomic alterations (SGAs) in patient tumours has emerged as a new avenue of investigation, not only as a disease monitoring strategy, but also to improve our understanding of heterogeneity and clonal evolution from diagnosis through disease progression. Furthermore, analysis of circulating-free DNA (cfDNA) in the so-called "liquid biopsy" has emerged as a non-invasive method to identify genomic information to inform targeted therapy and may also capture the heterogeneity of the primary and metastatic tumours. Considering the potential of cfDNA analysis as a translational laboratory tool in clinical practice, establishing the extent to which cfDNA represents the SGAs of tumours, particularly actionable driver alterations, becomes a matter of importance, warranting standardisation of methods and practices. Here, we assess the utilisation of cfDNA for molecular profiling of SGAs in tumour tissue across a broad range of solid tumours. Moreover, we examine the underlying factors contributing to discordance of detected SGAs between cfDNA and tumour tissue.
Collapse
Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Lab blocks level 3, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Correspondence:
| | - Tara Hurst
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
| |
Collapse
|
14
|
Liao Y, Chen Y, Kou X, Xiao Y, Ye J, Wu A. Diagnostic test accuracy of droplet digital PCR for the detection of EGFR mutation (T790M) in plasma: Systematic review and meta-analysis. Clin Chim Acta 2019; 503:190-196. [PMID: 31805270 DOI: 10.1016/j.cca.2019.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/04/2019] [Accepted: 11/16/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND T790M mutation was a primary lead cause in the acquired resistance to EGFR-TKIs confirmed in earlier studies. Since the shortcomings of tumor tissue detection are well known, the liquid biopsy is more appropriate to track T790M status. We assessed the accuracy and clinical significance of the droplet digital PCR (ddPCR) detection of T790M mutation in plasma. METHODS We retrieved PubMed, Embase, Cochrane, and Web of science with no limitation of language and publication year. Summary sensitivity and specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio of detection of EGFR T790M status were calculated from extracted data from included articles. The summary receiver operating curve (SROC), diagnostic odds ratio (DOR), and the area under the summary receiver operating curve (AUC) was used to assess the overall diagnostic accuracy. I2 and meta-regression were used to evaluate heterogeneity and the source of heterogeneity, respectively. RESULT We identified 15 studies in the total search of 1364 reports, including 427 paired tissue and plasma samples. The pooled sensitivity and the pooled specificity were 0.68 (95% CI 0.61-0.75) and 0.85 (95% CI 0.75-0.91) by the bivariate model, respectively. The AUC and the pooled DOR were 0.78 (95% CI 0.74-0.81) and 12 (95% CI 7-22), respectively. None of the cofactors could account for the heterogeneity. CONCLUSION The plasma analysis is of a promising performance to screen EGFR-T790M mutation status by ddPCR.
Collapse
Affiliation(s)
- Yingyin Liao
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China
| | - Yuan Chen
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, No. 151 Yanjiangxi Road, Guangzhou, Guangdong, China
| | - Xiaoxia Kou
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China
| | - Yi Xiao
- The Fifth Affiliated Hospital of Guangzhou Medical University, No. 621 Gangwan Road, Guangzhou, Guangdong, China
| | - Junkai Ye
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, No. 151 Yanjiangxi Road, Guangzhou, Guangdong, China
| | - Aiwu Wu
- KingMed School of Laboratory Medicine of Guangzhou Medical University, No. 195 Dongfengxi Road, Guangzhou, Guangdong, China.
| |
Collapse
|
15
|
Hiemcke-Jiwa LS, Ten Dam-van Loon NH, Leguit RJ, Nierkens S, Ossewaarde-van Norel J, de Boer JH, Roholl FF, de Weger RA, Huibers MMH, de Groot-Mijnes JDF, Kuiper JJW. Potential Diagnosis of Vitreoretinal Lymphoma by Detection of MYD88 Mutation in Aqueous Humor With Ultrasensitive Droplet Digital Polymerase Chain Reaction. JAMA Ophthalmol 2019; 136:1098-1104. [PMID: 30027272 DOI: 10.1001/jamaophthalmol.2018.2887] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance The diagnostic workup of patients suspected of having vitreoretinal lymphoma (VRL) is primarily based on vitreous fluid analysis, including the recently emerging myeloid differentiation primary response gene 88 (MYD88) mutation analysis. Aqueous humor paracentesis is a relatively less invasive and safer procedure than taking vitreous fluid specimens, and aqueous humor-based MYD88 mutation analysis would provide an additional liquid biopsy tool to diagnose and monitor patients with VRL. Objective To investigate whether the detection of MYD88 L265P by highly sensitive droplet digital polymerase chain reaction (ddPCR) is feasible in the vitreous fluid and aqueous humor of patients with VRL. Design, Setting, and Participants This cohort study includes aqueous humor and vitreous fluid samples from patients with VRL who were treated at the University Medical Center Utrecht, in Utrecht, the Netherlands, from August 2005 to August 2017. Ocular fluids were randomized and masked before MYD88 L265P analysis, which was performed using an in-house validated ddPCR platform. Patients with uveitis were included as a comparison group. Main Outcomes and Measures The presence of MYD88 L265P mutation detected by ddPCR in AH and VF. Results The study included 96 samples from 63 individuals, including 23 patients with VRL (of whom 10 were female and 13 male, with a mean [SD] age of 72 [7.3] years) and 40 individuals with uveitis (of whom 23 were female and 17 male, with a mean [SD] age of 58 [20.9] years). In 17 of 23 patients with VRL (74%), MYD88 L265P was detected; it was not detected in any of the patients with uveitis. It was detectable in both vitreous fluid and aqueous humor samples. In the paired samples, the mutation was detected in 8 of 9 aqueous humor samples (89%) of the MYD88 L265P-positive vitreous fluid samples. In vitreous fluid, the MYD88 ddPCR test showed a sensitivity of 75% (95% CI, 50%-92%) and a positive predictive value of 100%; in aqueous humor, sensitivity was 67% (95% CI, 42%-92%), and positive predictive value was 100%. Specificity was 100% in both fluids. After treatment, the mutation was no longer detectable in any ocular fluids. Conclusions and Relevance The high concordance between aqueous humor and vitreous fluid samples suggests that use of the easily accessible aqueous humor is nearly as informative as vitreous fluid in the identification of key somatic mutations in patients with VRL. This approach may provide an additional minimally invasive tool for accurate diagnosis, detection of recurrence, and monitoring of treatment.
Collapse
Affiliation(s)
- Laura S Hiemcke-Jiwa
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Roos J Leguit
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan Nierkens
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Joke H de Boer
- Deparment of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Floor F Roholl
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Roel A de Weger
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Jonas J W Kuiper
- Deparment of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| |
Collapse
|
16
|
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]
|
17
|
Hanibuchi M, Kanoh A, Kuramoto T, Saito T, Tobiume M, Saijo A, Kozai H, Kondo M, Morizumi S, Yoneda H, Kagawa K, Ogino H, Sato S, Kawano H, Otsuka K, Toyoda Y, Nokihara H, Goto H, Nishioka Y. Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA. Oncotarget 2019; 10:3654-3666. [PMID: 31217900 PMCID: PMC6557207 DOI: 10.18632/oncotarget.26951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
The feasibility and required sensitivity of circulating free DNA (cfDNA)-based detection methods in second-line epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment are not well elucidated. We examined T790M and other activating mutations of EGFR by cfDNA to assess the clinical usability. In 45 non-small cell lung cancer (NSCLC) patients harboring activating EGFR mutations, cfDNAs were prepared from the plasma samples. EGFR mutations in cfDNA were detected using highly sensitive methods and originally developed assays and these results were compared to tissue-based definitive diagnoses. The specificity of each cfDNA-based method ranged 96–100% whereas the sensitivity ranged 56–67%, indicating its low pseudo-positive rate. In EGFR-TKI failure cohort, 41–46% samples were positive for T790M by each cfDNA-based method, which was comparable to re-biopsy tissue-based T790M positive rates in literature. The concordance of the results for each EGFR mutation ranged from 83–95%. In eight patients, the results of the cfDNA-based assays and re-biopsy-derived tissue-based test were compared. The observed overall agreement ranged in 50–63% in T790M, and in 63–100% in activating EGFR mutations. In this study, we have newly developed three types of assay which have enough sensitivity to detect cfDNA. We also detected T790M in 44% of patients who failed prior EGFR-TKI treatment, indicating that cfDNA-based assay has clinical relevance for detecting acquired mutations of EGFR.
Collapse
Affiliation(s)
- Masaki Hanibuchi
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan.,Department of Internal Medicine, Shikoku Central Hospital of the Mutual Aid Association of Public School Teachers, Shikoku-Chuo, 799-0193, Japan
| | - Akira Kanoh
- Biomarker Research, Early Development Strategy and Planning, Taiho Pharmaceutical Co., Ltd., Tsukuba, 300-2611, Japan
| | - Takuya Kuramoto
- Biomarker Research, Early Development Strategy and Planning, Taiho Pharmaceutical Co., Ltd., Tsukuba, 300-2611, Japan
| | - Tatsuro Saito
- Riken Genesis Co., Ltd., Shinagawa-ku, Tokyo, 141-0032, Japan
| | - Makoto Tobiume
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Atsuro Saijo
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroyuki Kozai
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Mayo Kondo
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Shun Morizumi
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroto Yoneda
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Kozo Kagawa
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hirokazu Ogino
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Seidai Sato
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroshi Kawano
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Kenji Otsuka
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Yuko Toyoda
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroshi Nokihara
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hisatsugu Goto
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Yasuhiko Nishioka
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| |
Collapse
|
20
|
Demuth C, Winther-Larsen A, Madsen AT, Meldgaard P, Sorensen BS. A method for treatment monitoring using circulating tumour DNA in cancer patients without targetable mutations. Oncotarget 2018; 9:31066-31076. [PMID: 30123427 PMCID: PMC6089565 DOI: 10.18632/oncotarget.25779] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/12/2018] [Indexed: 02/05/2023] Open
Abstract
Background The potentials of circulating tumour DNA (ctDNA) have been studied for non-invasive disease monitoring in patients with targetable mutations. However, the majority of cancer patients harbour no targetable mutations. A workflow including targeted next-generation sequencing (NGS) and droplet digital PCR (ddPCR) could be used for monitoring treatment in these patients. Thus, our aim was to evaluate the workflow for ctDNA monitoring in a cohort of non-small cell lung cancer patients. Methods Forty patients were prospectively included. Plasma samples were collected prior to and during treatment. NGS (Ion AmpliSeq Colon and Lung Cancer panel v2) was performed on ctDNA from pre-treatment samples. The identified mutations were monitored by ddPCR in consecutively collected samples. Results Mutations were detected in 21 patients. The most commonly mutated genes were TP53 (N=20) and KRAS (N=13). Treatment was discontinued due to non-response in 18 patients. In 16 of these, a simultaneous increase in ctDNA concentration was observed. A twofold ctDNA concentration increase confirmed in a second successive sample predicted non-response on the following imaging in 83% of patients (10/12). Conclusion ctDNA monitoring can be used for early detection of non-response in patients without targetable mutations, and therefore could supplement imaging data for treatment monitoring in this subset of patients.
Collapse
Affiliation(s)
- Christina Demuth
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Winther-Larsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Tranberg Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
21
|
Extracellular vesicles and ctDNA in lung cancer: biomarker sources and therapeutic applications. Cancer Chemother Pharmacol 2018; 82:171-183. [PMID: 29948020 DOI: 10.1007/s00280-018-3586-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/20/2018] [Indexed: 02/05/2023]
Abstract
Lung cancer is the leading cause of cancer death in the world. Recently, targeted therapy and anti-programmed cell death receptor 1 (PD-1) and anti-programmed cell death ligand 1 (PD-L1) immunotherapy have made great progress in treatment of lung cancer. However, responses to these therapies are variable, influenced by genetic alterations, high microsatellite instability and mismatch repair deficiency. Liquid biopsy of extracellular vesicles and circulating tumor DNA (ctDNA) emerges as a new promising non-invasive means that enables not only biomarker determination, but also continuous monitoring of cancer treatment. Notably, tumor extracellular vesicles play important roles in tumor formation and progression, and also serve as natural carriers for anti-tumor drugs and short-interfering RNA. In this review, we summarize the latest progress in understanding the relationships of extracellular vesicles and ctDNA in cancer biology, diagnosis and drug delivery. In particular, the application of extracellular vesicles and ctDNA in anti-PD-1/PD-L1 immunotherapy is discussed.
Collapse
|
22
|
Zhang R, Chen B, Tong X, Wang Y, Wang C, Jin J, Tian P, Li W. Diagnostic accuracy of droplet digital PCR for detection of EGFR T790M mutation in circulating tumor DNA. Cancer Manag Res 2018; 10:1209-1218. [PMID: 29844700 PMCID: PMC5962302 DOI: 10.2147/cmar.s161382] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objectives Although different methods have been established to detect epidermal growth factor receptor (EGFR) T790M mutation in circulating tumor DNA (ctDNA), a wide range of diagnostic accuracy values were reported in previous studies. The aim of this meta-analysis was to provide pooled diagnostic accuracy measures for droplet digital PCR (ddPCR) in the diagnosis of EGFR T790M mutation based on ctDNA. Materials and methods A systematic review and meta-analysis were carried out based on resources from Pubmed, Web of Science, Embase and Cochrane Library up to October 11, 2017. Data were extracted to assess the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio (NLR), diagnostic OR (DOR), and areas under the summary receiver-operating characteristic curve (SROC). Results Eleven of 311 studies identified have met the including criteria. The sensitivity and specificity of ddPCR for the detection of T790M mutation in ctDNA ranged from 0.0% to 100.0% and 63.2% to 100.0%, respectively. For the pooled analysis, ddPCR had a performance of 70.1% (95% CI, 62.7%–76.7%) sensitivity, 86.9 % (95% CI, 80.6%–91.7%) specificity, 3.67 (95% CI, 2.33–5.79) PLR, 0.41 (95% CI, 0.32–0.55) NLR, and 10.83 (95% CI, 5.86–20.03) DOR, with the area under the SROC curve being 0.82. Conclusion The ddPCR harbored a good performance for detection of EGFR T790M mutation in ctDNA.
Collapse
Affiliation(s)
- Rui Zhang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Bojiang Chen
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xiang Tong
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ye Wang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Lung Cancer Treatment Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Jing Jin
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Panwen Tian
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Lung Cancer Treatment Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| |
Collapse
|
23
|
Abraham J, Singh S, Joshi S. Liquid biopsy - emergence of a new era in personalized cancer care. ACTA ACUST UNITED AC 2018. [DOI: 10.1186/s41241-018-0053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|