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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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52
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An J, Tang CH, Wang N, Liu Y, Lv J, Xu B, Li XY, Guo WF, Gao HJ, He K, Liu XQ. Serum peptide expression and treatment responses in patients with advanced non-small-cell lung cancer. Oncol Lett 2018; 15:9307-9316. [PMID: 29844828 DOI: 10.3892/ol.2018.8460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/19/2018] [Indexed: 11/05/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) mutation is an important predictor for response to personalized treatments of patients with advanced non-small-cell lung cancer (NSCLC). However its usage is limited due to the difficult of obtaining tissue specimens. A novel prediction system using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a perspective tool in European countries to identify patients who are likely to benefit from EGFR tyrosine kinase inhibitor (TKI) treatment. In the present study, MALDI-TOF MS was used on pretreatment serum samples of patients with advanced non-small-cell lung cancer to discriminate the spectra between disease control and disease progression groups in one cohort of Chinese patients. The candidate features for classification were subsequently validated in a blinded fashion in another set of patients. The correlation between plasma EGFR mutation status and the intensities of representative spectra for classification was evaluated. A total of 103 patients that were treated with EGFR-TKIs were included. It was determined that 8 polypeptides peaks were significant different between the disease control and disease progression group. A total of 6 polypeptides were established in the classification algorithm. The sensitivity of the algorithm to predict treatment responses was 76.2% (16/21) and the specificity was 81.8% (18/22). The accuracy rate of the algorithm was 79.1% (34/43). A total of 3 polypeptides were significantly correlated with EGFR mutations (P=0.04, P=0.03 and P=0.04, respectively). The present study confirmed that MALDI-TOF MS analysis can be used to predict responses to EGFR-TKI treatment of the Asian population where the EGFR mutation status differs from the European population. Furthermore, the expression intensities of the three polypeptides in the classification model were associated with EGFR mutation.
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Affiliation(s)
- Juan An
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China.,Department of Oncology, The General Hospital of PLA Rocket Force, Beijing 100088, P.R. China
| | - Chuan-Hao Tang
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Na Wang
- National Center of Biomedical Analysis, Academy of Military Medical Sciences, Beijing 100850, P.R. China
| | - Yi Liu
- Department of Oncology, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Jin Lv
- Department of Oncology, The General Hospital of PLA Rocket Force, Beijing 100088, P.R. China
| | - Bin Xu
- National Center of Biomedical Analysis, Academy of Military Medical Sciences, Beijing 100850, P.R. China
| | - Xiao-Yan Li
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Wan-Feng Guo
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Hong-Jun Gao
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Kun He
- National Center of Biomedical Analysis, Academy of Military Medical Sciences, Beijing 100850, P.R. China
| | - Xiao-Qing Liu
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
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53
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O'Connell GC, Chantler PD, Barr TL. High Interspecimen Variability in Nucleic Acid Extraction Efficiency Necessitates the Use of Spike-In Control for Accurate qPCR-based Measurement of Plasma Cell-Free DNA Levels. Lab Med 2018; 48:332-338. [PMID: 29036313 DOI: 10.1093/labmed/lmx043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Objective To assess the interspecimen variability associated with plasma DNA extraction in order to provide insight regarding the necessity to use an exogenous spike-in control when measuring cell-free DNA (cfDNA) levels using quantitative polymerase chain reaction (qPCR). Methods Plasma specimens were obtained from 8 healthy individuals, 20 patients with cardiovascular disease risk factors, and 54 patients diagnosed with acute stroke. Specimens were spiked with an exogenous oligonucleotide fragment, and total DNA was extracted via automated solid phase anion exchange. We determined recovery of the exogenous fragment via qPCR and used this information to calculate DNA extraction efficiency. Results Plasma DNA extraction efficiencies varied dramatically between specimens, ranging from 22.9% to 88.1%, with a coefficient of variance of 28.9%. No significant differences in DNA extraction efficiencies were observed between patient populations. Conclusions We strongly recommend the use of an exogenous spike-in control to account for variance in plasma DNA extraction efficiency when assessing cell free DNA (cfDNA) levels by qPCR in future biomarker investigations.
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Affiliation(s)
- Grant C O'Connell
- Center for Basic and Translational Stroke Research, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia.,Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Paul D Chantler
- Center for Cardiovascular and Respiratory Sciences, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia.,Division of Exercise Physiology, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Taura L Barr
- Valtari Bio Incorporated, Morgantown, West Virginia
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54
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Mao X, Chen Z, Zhao Y, Yu Y, Guan S, Woodfield SE, Vasudevan SA, Tao L, Pang JC, Lu J, Zhang H, Zhang F, Yang J. Novel multi-targeted ErbB family inhibitor afatinib blocks EGF-induced signaling and induces apoptosis in neuroblastoma. Oncotarget 2018; 8:1555-1568. [PMID: 27902463 PMCID: PMC5352076 DOI: 10.18632/oncotarget.13657] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. The ErbB family of proteins is a group of receptor tyrosine kinases that promote the progression of various malignant cancers including neuroblastoma. Thus, targeting them with small molecule inhibitors is a promising strategy for neuroblastoma therapy. In this study, we investigated the anti-tumor effect of afatinib, an irreversible inhibitor of members of the ErbB family, on neuroblastoma. We found that afatinib suppressed the proliferation and colony formation ability of neuroblastoma cell lines in a dose-dependent manner. Afatinib also induced apoptosis and blocked EGF-induced activation of PI3K/AKT/mTOR signaling in all neuroblastoma cell lines tested. In addition, afatinib enhanced doxorubicin-induced cytotoxicity in neuroblastoma cells, including the chemoresistant LA-N-6 cell line. Finally, afatinib exhibited antitumor efficacy in vivo by inducing apoptosis in an orthotopic xenograft neuroblastoma mouse model. Taken together, these results show that afatinib inhibits neuroblastoma growth both in vitro and in vivo by suppressing EGFR-mediated PI3K/AKT/mTOR signaling. Our study supports the idea that EGFR is a potential therapeutic target in neuroblastoma. And targeting ErbB family protein kinases with small molecule inhibitors like afatinib alone or in combination with doxorubicin is a viable option for treating neuroblastoma.
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Affiliation(s)
- Xinfang Mao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, P. R. China.,Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhenghu Chen
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P. R. China
| | - Yanling Zhao
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yang Yu
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shan Guan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, P. R. China.,Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah E Woodfield
- Division of Pediatric Surgery, Texas Children's Hospital Department of Surgery, Michael E. DeBakey Department of Surgery, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sanjeev A Vasudevan
- Division of Pediatric Surgery, Texas Children's Hospital Department of Surgery, Michael E. DeBakey Department of Surgery, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ling Tao
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jonathan C Pang
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jiaxiong Lu
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huiyuan Zhang
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, P. R. China
| | - Jianhua Yang
- Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
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55
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Nishikawa S, Kimura H, Koba H, Yoneda T, Watanabe S, Sakai T, Hara J, Sone T, Kasahara K, Nakao S. Selective gene amplification to detect the T790M mutation in plasma from patients with advanced non-small cell lung cancer (NSCLC) who have developed epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) resistance. J Thorac Dis 2018; 10:1431-1439. [PMID: 29707292 DOI: 10.21037/jtd.2018.01.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background The epidermal growth factor receptor (EGFR) T790M mutation is associated with resistance to EGFR tyrosine kinase inhibitors (EGFR-TKIs) in non-small cell lung cancer (NSCLC). However, tissues for the genotyping of the EGFR T790M mutation can be difficult to obtain in a clinical setting. The aims of this study were to evaluate a blood-based, non-invasive approach to detecting the EGFR T790M mutation in advanced NSCLC patients using the PointMan™ EGFR DNA enrichment kit, which is a novel method for the selective amplification of specific genotype sequences. Methods Blood samples were collected from NSCLC patients who had activating EGFR mutations and who were resistant to EGFR-TKI treatment. Using cell-free DNA (cfDNA) from plasma, EGFR T790M mutations were amplified using the PointMan™ enrichment kit, and all the reaction products were confirmed using direct sequencing. The concentrations of plasma DNA were then determined using quantitative real-time PCR. Results Nineteen patients were enrolled, and 12 patients (63.2%) were found to contain EGFR T790M mutations in their cfDNA, as detected by the kit. T790M mutations were detected in tumor tissues in 12 cases, and 11 of these cases (91.7%) also exhibited the T790M mutation in cfDNA samples. The concentrations of cfDNA were similar between patients with the T790M mutation and those without the mutation. Conclusions The PointMan™ kit provides a useful method for determining the EGFR T790M mutation status in cfDNA.
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Affiliation(s)
- Shingo Nishikawa
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hideharu Kimura
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hayato Koba
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Taro Yoneda
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Satoshi Watanabe
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Tamami Sakai
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Johsuke Hara
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Takashi Sone
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Kazuo Kasahara
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Shinji Nakao
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
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56
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Acquired savolitinib resistance in non-small cell lung cancer arises via multiple mechanisms that converge on MET-independent mTOR and MYC activation. Oncotarget 2018; 7:57651-57670. [PMID: 27472392 PMCID: PMC5295379 DOI: 10.18632/oncotarget.10859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the most common cause of cancer death globally with a significant, unmet need for more efficacious treatments. The receptor tyrosine kinase MET has been implicated as an oncogene in numerous cancer subtypes, including non-small cell lung cancer (NSCLC). Here we explore the therapeutic potential of savolitinib (volitinib, AZD6094, HMPL-504), a potent and selective MET inhibitor, in NSCLC. In vitro, savolitinib inhibits MET phosphorylation with nanomolar potency, which correlates with blockade of PI3K/AKT and MAPK signaling as well as MYC down-regulation. In vivo, savolitinib causes inhibition of these pathways and significantly decreases growth of MET-dependent xenografts. To understand resistance mechanisms, we generated savolitinib resistance in MET-amplified NSCLC cell lines and analyzed individual clones. We found that upregulation of MYC and constitutive mTOR pathway activation is a conserved feature of resistant clones that can be overcome by knockdown of MYC or dual mTORC1/2 inhibition. Lastly, we demonstrate that mechanisms of resistance are heterogeneous, arising via a switch to EGFR dependence or by a requirement for PIM signaling. This work demonstrates the efficacy of savolitinib in NSCLC and characterizes acquired resistance, identifying both known and novel mechanisms that may inform combination strategies in the clinic.
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57
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Morikawa A, Hayashi T, Shimizu N, Kobayashi M, Taniue K, Takahashi A, Tachibana K, Saito M, Kawabata A, Iida Y, Ueda K, Saito M, Yanaihara N, Tanabe H, Yamada K, Takano H, Nureki O, Okamoto A, Akiyama T. PIK3CA and KRAS mutations in cell free circulating DNA are useful markers for monitoring ovarian clear cell carcinoma. Oncotarget 2018; 9:15266-15274. [PMID: 29632642 PMCID: PMC5880602 DOI: 10.18632/oncotarget.24555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) exhibits distinct phenotypes, such as resistance to chemotherapy, poor prognosis and an association with endometriosis. Biomarkers and imaging techniques currently in use are not sufficient for reliable diagnosis of this tumor or prediction of therapeutic response. It has recently been reported that analysis of somatic mutations in cell-free circulating DNA (cfDNA) released from tumor tissues can be useful for tumor diagnosis. In the present study, we attempted to detect mutations in PIK3CA and KRAS in cfDNA from OCCC patients using droplet digital PCR (ddPCR). Here we show that we were able to specifically detect PIK3CA-H1047R and KRAS-G12D in cfDNA from OCCC patients and monitor their response to therapy. Furthermore, we found that by cleaving wild-type PIK3CA using the CRISPR/Cas9 system, we were able to improve the sensitivity of the ddPCR method and detect cfDNA harboring PIK3CA-H1047R. Our results suggest that detection of mutations in cfDNA by ddPCR would be useful for the diagnosis of OCCC, and for predicting its recurrence.
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Affiliation(s)
- Asuka Morikawa
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Tomoatsu Hayashi
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Naomi Shimizu
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mana Kobayashi
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kenzui Taniue
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Akiko Takahashi
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kota Tachibana
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Misato Saito
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Ayako Kawabata
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Yasushi Iida
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Kazu Ueda
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Motoaki Saito
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Nozomu Yanaihara
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Hiroshi Tanabe
- Department of Obstetrics and Gynecology, Jikei University, Kashiwa Hospital, Chiba, Japan
| | - Kyosuke Yamada
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Hirokuni Takano
- Department of Obstetrics and Gynecology, Jikei University, Kashiwa Hospital, Chiba, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
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58
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Yang M, Forbes ME, Bitting RL, O'Neill SS, Chou PC, Topaloglu U, Miller LD, Hawkins GA, Grant SC, DeYoung BR, Petty WJ, Chen K, Pasche BC, Zhang W. Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system? Ann Oncol 2018; 29:311-323. [PMID: 29216340 PMCID: PMC5834142 DOI: 10.1093/annonc/mdx766] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation. Recent work highlights circulating tumor DNA (ctDNA) present in the blood as a supplemental, or perhaps an alternative, source of DNA to identify the clinically relevant cancer mutational landscape. Indeed, this noninvasive approach may facilitate repeated monitoring of disease progression and treatment response, serving as a means to guide targeted therapies based on detected actionable mutations in patients with advanced or metastatic solid tumors. Notably, ctDNA is heralding a revolution in the range of genomic profiling and molecular mechanisms to be utilized in the battle against cancer. This review will discuss the biology of ctDNA, current methods of detection and potential applications of this information in tumor diagnosis, treatment, and disease prognosis. Conventional classification of tumors to describe cancer stage follow the TNM notation system, heavily weighting local tumor extent (T), lymph node invasion (N), and detectable metastasis (M). With recent advancements in genomics and bioinformatics, it is conceivable that routine analysis of ctDNA from liquid biopsy (B) may make cancer diagnosis, treatment, and prognosis more accurate for individual patients. We put forward the futuristic concept of TNMB tumor classification, opening a new horizon for precision medicine with the hope of creating better outcomes for cancer patients.
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Affiliation(s)
- M Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - M E Forbes
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - R L Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - S S O'Neill
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - P-C Chou
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - U Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - L D Miller
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - G A Hawkins
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, USA
| | - S C Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - B R DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - W J Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - K Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| | - B C Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - W Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA.
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59
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Qian X, Liu J, Sun Y, Wang M, Lei H, Luo G, Liu X, Xiong C, Liu D, Liu J, Tang Y. Circulating cell-free DNA has a high degree of specificity to detect exon 19 deletions and the single-point substitution mutation L858R in non-small cell lung cancer. Oncotarget 2018; 7:29154-65. [PMID: 27081078 PMCID: PMC5045385 DOI: 10.18632/oncotarget.8684] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
Detection of an epidermal growth factor receptor (EGFR) mutation in circulating cell-free DNA (cfDNA) is a noninvasive method to collect genetic information to guide treatment of lung cancer with tyrosine-kinase inhibitors (TKIs). However, the association between cfDNA and detection of EGFR mutations in tumor tissue remains unclear. Here, a meta-analysis was performed to determine whether cfDNA could serve as a substitute for tissue specimens for the detection of EGFR mutations. The pooled sensitivity, specificity, and areas under the curve of cfDNA were 0.60, 0.94, and 0.9208 for the detection of EGFR mutations, 0.64, 0.99, and 0.9583 for detection of the exon 19 deletion, and 0.57, 0.99, and 0.9605 for the detection of the L858R mutation, respectively. Our results showed that cfDNA has a high degree of specificity to detect exon 19 deletions and L858R mutation. Due to its high specificity and noninvasive characteristics, cfDNA analysis presents a promising method to screen for mutations in NSCLC and predict patient response to EGFR-TKI treatment, dynamically assess treatment outcome, and facilitate early detection of resistance mutations.
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Affiliation(s)
- Xin Qian
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Jia Liu
- Department of Orthopedic, Lanzhou University First Hospital, Lanzhou, 730000, Gansu, P.R. China
| | - Yuhui Sun
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Meifang Wang
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Huaiding Lei
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Guoshi Luo
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Xianjun Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Chang Xiong
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Dan Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Jie Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Yijun Tang
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
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60
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Goldman JW, Noor ZS, Remon J, Besse B, Rosenfeld N. Are liquid biopsies a surrogate for tissue EGFR testing? Ann Oncol 2018; 29:i38-i46. [PMID: 29462257 DOI: 10.1093/annonc/mdx706] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Molecular profiling has changed the treatment landscape in advanced non-small-cell lung cancer. Accurately identifying the tumours that harbour sensitizing EGFR mutations, the most common targetable molecular alteration, as well as those with acquired resistance mutations (e.g. T790M) on treatment is a high clinical priority. The current clinical gold standard is genotyping of tumour specimens. However, the practical utility of this approach is limited by the lack of available tissue and the potential complications associated with biopsies. With the advent of newer sequencing assays, it has become feasible to assess tumour genomics via a blood sample, termed a 'liquid biopsy'. In this review, we summarize the available techniques for liquid biopsies and their applicability for detecting sensitizing and resistance EGFR mutations and how these results may be used for making treatment decisions.
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Affiliation(s)
- J W Goldman
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - Z S Noor
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - J Remon
- Department of Oncology Medicine, Gustave Roussy, Villejuif
| | - B Besse
- Department of Oncology Medicine, Gustave Roussy, Villejuif
- University Paris-Sud, Orsay, France
| | - N Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
- Cancer Research UK Major Centre - Cambridge, Cambridge, UK
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61
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Veldore VH, Choughule A, Routhu T, Mandloi N, Noronha V, Joshi A, Dutt A, Gupta R, Vedam R, Prabhash K. Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer. LUNG CANCER (AUCKLAND, N.Z.) 2018; 9:1-11. [PMID: 29379323 PMCID: PMC5757203 DOI: 10.2147/lctt.s147841] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA), from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS) for EGFR mutation testing in non-small cell lung cancer (NSCLC). A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96%) between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically useful material for molecular testing in NSCLC.
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Affiliation(s)
| | | | | | | | | | - Amit Joshi
- Tata Memorial Centre, Parel, Mumbai, India
| | - Amit Dutt
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India
| | - Ravi Gupta
- MedGenome Labs Private Ltd,, Bangalore, India
| | - Ramprasad Vedam
- MedGenome Labs Private Ltd,, Bangalore, India
- Ramprasad Vedam, MedGenome Labs Private Ltd., 3 Floor, Narayana Netralaya Building, NH City, 258/A, Bommasandra Industrial Area, Bommasandra, Bangalore 560099, India, Email
| | - Kumar Prabhash
- Tata Memorial Centre, Parel, Mumbai, India
- Correspondence: Kumar Prabhash, Department of Medical Oncology, Tata Memorial Hospital, Dr E Borges Road, Parel, Mumbai 400 012, India, Email
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62
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Westover D, Zugazagoitia J, Cho BC, Lovly CM, Paz-Ares L. Mechanisms of acquired resistance to first- and second-generation EGFR tyrosine kinase inhibitors. Ann Oncol 2018; 29:i10-i19. [PMID: 29462254 PMCID: PMC6454547 DOI: 10.1093/annonc/mdx703] [Citation(s) in RCA: 424] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Patients with non-small-cell lung cancer (NSCLC) whose tumours harbour activating mutations within the epidermal growth factor receptor (EGFR) frequently derive significant clinical and radiographic benefits from treatment with EGFR tyrosine kinase inhibitors (TKIs). As such, prospective identification of EGFR mutations is now the standard of care worldwide. However, acquired therapeutic resistance to these agents invariably develops. Over the past 10 years, great strides have been made in defining the molecular mechanisms of EGFR TKI resistance in an effort to design rational strategies to overcome this acquired drug resistance. Approximately 60% of patients with acquired resistance to the EGFR TKIs (erlotinib, gefitinib, and afatinib) develop a new mutation within the drug target. This mutation-T790M-has been shown to alter drug binding and enzymatic activity of the mutant EGF receptor. Less common mechanisms of acquired resistance include MET amplification, ERBB2 amplification, transformation to small-cell lung cancer, and others. Here, we present a condensed overview of the literature on EGFR-mutant NSCLC, paying particular attention to mechanisms of drug resistance, recent clinical trial results, and novel strategies for identifying and confronting drug resistance, while also striving to identify gaps in current knowledge. These advances are rapidly altering the treatment landscape for EGFR-mutant NSCLC, expanding the armamentarium of available therapies to maximize patient benefit.
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Affiliation(s)
- D Westover
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
| | - J Zugazagoitia
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid
- Instituto de Investigación i + 12, Madrid
- Lung Cancer Group, Clinical Research Program, CNIO, Madrid
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - B C Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - C M Lovly
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
- Department of Cancer Biology
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, USA
| | - L Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid
- Instituto de Investigación i + 12, Madrid
- Lung Cancer Group, Clinical Research Program, CNIO, Madrid
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
- Complutense University, Madrid, Spain
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63
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Chen Y, Guo W, Fan J, Chen Y, Zhang X, Chen X, Luo P. The applications of liquid biopsy in resistance surveillance of anaplastic lymphoma kinase inhibitor. Cancer Manag Res 2017; 9:801-811. [PMID: 29263703 PMCID: PMC5724713 DOI: 10.2147/cmar.s151235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With the clinical promotion of precision medicine and individualized medical care, molecular targeted medicine has been used to treat non-small cell lung cancer (NSCLC) patients and proved to be significantly effective. Anaplastic lymphoma kinase (ALK) inhibitor is one of the most important specific therapeutic agents for patients with ALK-positive NSCLC. It can extend the survival of patients. However, resistance to the ALK inhibitor inevitably develops in the application process. So, the real-time resistance surveillance is particularly important, and liquid biopsy is one of the most potential inspection methods. Circulating tumor cells, circulating free tumor DNA and exosome in body fluid are used as the main detection biomarkers to reflect the occurrence of resistance in real time through sequencing or counting and then to guide the follow-up treatment.
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Affiliation(s)
- Yating Chen
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Wenjie Guo
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Junsheng Fan
- Department of Respiratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Yuqing Chen
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Xiaoli Zhang
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Xin Chen
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Peng Luo
- Department of Respiratory, Zhujiang Hospital of Southern Medical University, Guangzhou, China
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64
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A case of resistance to tyrosine kinase inhibitor therapy: small cell carcinoma transformation concomitant with plasma-genotyped T790M positivity. Anticancer Drugs 2017; 28:1056-1061. [PMID: 28723866 PMCID: PMC5610567 DOI: 10.1097/cad.0000000000000540] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although non-small-cell lung cancer patients with epidermal growth factor receptor (EGFR) mutations are responsive to EGFR-tyrosine kinase inhibitors, drug resistances are always inevitable. The secondary somatic EGFR threonine-methionine substitution at position 790 (T790M) mutation accounts for ∼50% of acquired resistance mechanisms. Small cell lung cancer (SCLC) transformation is a relatively rare mechanism, but has recently attracted considerable attention. The coexistence of both the mechanisms in one patient is much more scarce in clinic. In this case report, we described a 37-year-old woman who underwent refractory after second-line gefitinib therapy and was confirmed to have SCLC transformation without the T790M mutation in the left lobar nodule, but concomitant with the plasma-genotyped EGFR T790M mutation. Our case report uncovered the underling relationship between SCLC transformation and the T790M mutation, and the fluid biopsy approach may help overcome the problem of heterogeneity in acquired resistance to EGFR-tyrosine kinase inhibitors.
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65
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Oh E, Jeong HM, Kwon MJ, Ha SY, Park HK, Song JY, Kim YJ, Choi JS, Lee EH, Lee J, Choi YL, Shin YK. Unforeseen clonal evolution of tumor cell population in recurrent and metastatic dermatofibrosarcoma protuberans. PLoS One 2017; 12:e0185826. [PMID: 28977029 PMCID: PMC5627939 DOI: 10.1371/journal.pone.0185826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/20/2017] [Indexed: 02/03/2023] Open
Abstract
Dermatofibrosarcoma protuberans (DFSP) is a very rare soft tissue sarcoma, generally of low-grade malignancy. DFSP is locally aggressive with a high recurrence rate, but metastasis occurs rarely. To investigate the mechanism of metastasis in DFSP, we analyzed the whole exome sequencing data of serial tumor samples obtained from a patient who had a 10-year history of recurrent and metastatic DFSP. Tracking various genomic alterations, namely somatic mutations, copy number variations, and chromosomal rearrangements, we observed a dramatic change in tumor cell population during the occurrence of metastasis in this DFSP case. The new subclone that emerged in metastatic DFSP harbored a completely different set of somatic mutations and new focal amplifications, which had not been observed in the primary clone before metastasis. The COL1A1-PDGFB fusion, characteristic of DFSP, was found in all of the serial samples. Moreover, the break position on the fusion gene was identical in all samples. Based on these observations, we suggest a clonal evolution model to explain the mechanism underlying metastasis in DFSP and identified several candidate target genes responsible for metastatic DFSP by utilizing The Cancer Genome Atlas database. This is the first study to observe clonal evolution in metastatic DFSP and provide insight for a possible therapeutic strategy for imatinib-resistant or metastatic DFSP.
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Affiliation(s)
- Ensel Oh
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyung Kyu Park
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Young Song
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Seoul, Korea
| | - Yu Jin Kim
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Seoul, Korea
| | - Jong-Sun Choi
- Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Eun Hee Lee
- Department of Pathology, Changwon Samsung Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
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66
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Liquid biopsy genotyping in lung cancer: ready for clinical utility? Oncotarget 2017; 8:18590-18608. [PMID: 28099915 PMCID: PMC5392351 DOI: 10.18632/oncotarget.14613] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy.
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67
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Lv X, Zhao M, Yi Y, Zhang L, Guan Y, Liu T, Yang L, Chen R, Ma J, Yi X. Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. J Vis Exp 2017. [PMID: 28872127 DOI: 10.3791/56342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The analysis of circulating tumor DNA (ctDNA) using next-generation sequencing (NGS) has become a valuable tool for the development of clinical oncology. However, the application of this method is challenging due to its low sensitivity in analyzing the trace amount of ctDNA in the blood. Furthermore, the method may generate false positive and negative results from this sequencing and subsequent analysis. To improve the feasibility and reliability of ctDNA detection in the clinic, here we present a technique which enriches rare mutations for sequencing, Enrich Rare Mutation Sequencing (ER-Seq). ER-Seq can distinguish a single mutation out of 1 x 107 wild-type nucleotides, which makes it a promising tool to detect extremely low frequency genetic alterations and thus will be very useful in studying disease heterogenicity. By virtue of the unique sequencing adapter's ligation, this method enables an efficient recovery of ctDNA molecules, while at the same time correcting for errors bidirectionally (sense and antisense). Our selection of 1021 kb probes enriches the measurement of target regions that cover over 95% of the tumor-related driver mutations in 12 tumors. This cost-effective and universal method enables a uniquely successful accumulation of genetic data. After efficiently filtering out background error, ER-seq can precisely detect rare mutations. Using a case study, we present a detailed protocol demonstrating probe design, library construction, and target DNA capture methodologies, while also including the data analysis workflow. The process to carry out this method typically takes 1-2 days.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xin Yi
- Geneplus-Beijing Institute;
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68
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Bernabé R, Hickson N, Wallace A, Blackhall FH. What do we need to make circulating tumour DNA (ctDNA) a routine diagnostic test in lung cancer? Eur J Cancer 2017; 81:66-73. [PMID: 28609695 DOI: 10.1016/j.ejca.2017.04.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/31/2017] [Accepted: 04/27/2017] [Indexed: 12/09/2022]
Abstract
The gold standard test for detection of epidermal growth factor receptor (EGFR) mutation is to genotype somatic DNA extracted from a tissue biopsy or cytology specimen. Yet, in at least 20% of patients this is not possible for various reasons including insufficient availability of neoplastic tissue, lack of fitness of the available tissue for a biopsy or that a biopsy is not technically feasible. Consequently, there has been intense investigation of circulating tumour DNA (ctDNA), released into the plasma fraction of blood from cancer cells during apoptosis/necrosis, as a minimally invasive 'liquid biopsy' and surrogate for cancer tissue. In 2014, the license for the EGFR tyrosine kinase inhibitor (EGFR-TKI), gefitinib, was updated to allow the use of plasma to determine EGFR mutation status in patients where tissue was not available. Then in 2016 the United States Food and Drug Administration (US FDA) approved the first companion diagnostic plasma EGFR test. Herein, we review the evidence for ctDNA as a diagnostic in patients with non-small cell lung cancer (NSCLC) and describe steps needed to incorporate such 'liquid biopsies' into everyday routine practice.
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Affiliation(s)
- Reyes Bernabé
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Medical Oncology Department, Hospital Virgen Del Rocio, Seville, Spain
| | - Nicholas Hickson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK
| | - Fiona Helen Blackhall
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Division of Molecular and Clinical Cancer Sciences, University of Manchester, Manchester, UK.
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69
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Liang Z, Cheng Y, Chen Y, Hu Y, Liu WP, Lu Y, Wang J, Wang Y, Wu G, Ying JM, Zhang HL, Zhang XC, Wu YL. EGFR T790M ctDNA testing platforms and their role as companion diagnostics: Correlation with clinical outcomes to EGFR-TKIs. Cancer Lett 2017. [PMID: 28642172 DOI: 10.1016/j.canlet.2017.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Somatic mutation in the epidermal growth factor receptor (EGFR) predict clinical response to EGFR tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC) and is a promising target for personalised medicine. EGFR mutations have prognostic value. Initially patients respond well to tyrosine kinase inhibitors but finally they would develop resistance and about 50% of this resistance can be attributed to the emergence of EGFR resistant mutation, T790M. This necessitates the need for genetic testing for clinical management of patients. Molecular testing has become the standard of care in patients with NSCLCs based on the recommendations of standard guidelines. Though there are several platforms for EGFR mutation detection, highly sensitive platforms for clinical applicability as companion diagnostics for ctDNA based testing are emerging. Due to the dynamic changes in the T790M mutation during tyrosine kinase inhibitor (TKI) treatment, real-time monitoring of these genetic alterations is mandate for planning treatment strategies. With the advent of third generation TKIs that potentially target T790M, improvement in clinical outcome is documented in patients with NSCLCs. Managing these outcomes with appropriate companion diagnostics using ctDNA in early detection of these genetic alterations will improve patient care.
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Affiliation(s)
- Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Cheng
- Department of Oncology, Jilin Provincial Cancer Hospital, Changchun, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanping Hu
- Department of Oncology, Hubei Cancer Hospital, Wuhan, China
| | - Wei-Ping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - You Lu
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Centre, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ye Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Ming Ying
- Department of Pathology, National Cancer Centre, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He-Long Zhang
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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70
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Sacher AG, Komatsubara KM, Oxnard GR. Application of Plasma Genotyping Technologies in Non-Small Cell Lung Cancer: A Practical Review. J Thorac Oncol 2017; 12:1344-1356. [PMID: 28611011 DOI: 10.1016/j.jtho.2017.05.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 10/19/2022]
Abstract
The rational treatment of metastatic NSCLC hinges on the timely detection of potentially targetable genomic alterations to guide therapy. Recent advances in highly sensitive genotyping technologies have allowed for development of novel plasma genotyping assays that are capable of noninvasively detecting targetable alterations in plasma cell-free DNA without reliance on traditional tissue genotyping. The rapid development of plasma genotyping has led to an explosion in the number of assay platforms available from both commercial and laboratory sources. The sheer number of such platforms has led to confusion among oncologists as to both the test characteristics and limitations of individual plasma genotyping assays and the clinical context in which these tests may be utilized either alone or in combination with traditional tissue genotyping. Reliable data from prospective validation against a tissue genotyping reference standard are available for only a limited number of platforms. Careful retrospective validation of alternative platforms utilizing paired tissue and plasma specimens collected under the auspices of clinical trials represent an alternative but reliable validation strategy. A consistent trend among these well-validated plasma genotyping assays has been the observation of high specificity and positive predictive value and more limited sensitivity. At present, validated assays can be considered actionable in instances in which a targetable genomic alteration is detected or an alternative nontargetable driver mutation is detected and can be used to infer the absence of one of the former.
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Affiliation(s)
- Adrian G Sacher
- Columbia University/New York-Presbyterian Hospital, New York, New York.
| | | | - Geoffrey R Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
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71
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Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer 2017; 17:223-238. [PMID: 28233803 DOI: 10.1038/nrc.2017.7] [Citation(s) in RCA: 1537] [Impact Index Per Article: 219.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Improvements in genomic and molecular methods are expanding the range of potential applications for circulating tumour DNA (ctDNA), both in a research setting and as a 'liquid biopsy' for cancer management. Proof-of-principle studies have demonstrated the translational potential of ctDNA for prognostication, molecular profiling and monitoring. The field is now in an exciting transitional period in which ctDNA analysis is beginning to be applied clinically, although there is still much to learn about the biology of cell-free DNA. This is an opportune time to appraise potential approaches to ctDNA analysis, and to consider their applications in personalized oncology and in cancer research.
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Affiliation(s)
- Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Charles Massie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, IDIBAPs, Carrer de Villarroel, 170 Barcelona 08036, Spain
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Richard Baird
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
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72
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Kwon BS, Park JH, Kim WS, Song JS, Choi CM, Rho JK, Lee JC. Predictive Factors for Switched EGFR-TKI Retreatment in Patients with EGFR-Mutant Non-Small Cell Lung Cancer. Tuberc Respir Dis (Seoul) 2017; 80:187-193. [PMID: 28416959 PMCID: PMC5392490 DOI: 10.4046/trd.2017.80.2.187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/12/2016] [Accepted: 02/09/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Third-generation tyrosine kinase inhibitors of the epidermal growth factor receptor (EGFR-TKIs) have proved efficacious in treating non-small cell lung cancer (NSCLC) patients with acquired resistance resulting from the T790M mutation. However, since almost 50% patients with the acquired resistance do not harbor the T790M mutation, retreatment with first- or second-generation EGFR-TKIs may be a more viable therapeutic option. Here, we identified positive response predictors to retreatment, in patients who switched to a different EGFR-TKI, following initial treatment failure. METHODS This study retrospectively reviewed the medical records of 42 NSCLC patients with EGFR mutations, whose cancers had progressed following initial treatment with gefitinib or erlotinib, and who had switched to a different first-generation EGFR-TKI during subsequent retreatment. To identify high response rate predictors in the changed EGFR-TKI retreatment, we analyzed the relationship between clinical and demographic parameters, and positive clinical outcomes, following retreatment with EGFR-TKI. RESULTS Overall, 30 (71.4%) patients received gefitinib and 12 (28.6%) patients received erlotinib as their first EGFR-TKI treatment. Following retreatment with a different EGFR-TKI, the overall response and disease control rates were 21.4% and 64.3%, respectively. There was no significant association between their overall responses. The median progression-free survival (PFS) after retreatment was 2.0 months. However, PFS was significantly longer in patients whose time to progression was ≥10 months following initial EGFR-TKI treatment, who had a mutation of exon 19, or whose treatment interval was <90 days. CONCLUSION In patients with acquired resistance to initial EGFR-TKI therapy, switched EGFR-TKI retreatment may be a salvage therapy for individuals possessing positive retreatment response predictors.
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Affiliation(s)
- Byoung Soo Kwon
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji Hyun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woo Sung Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Joon Seon Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang-Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Kyung Rho
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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73
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Circulating Tumor DNA for Mutation Detection and Identification of Mechanisms of Resistance in Non-Small Cell Lung Cancer. Mol Diagn Ther 2017; 21:375-384. [DOI: 10.1007/s40291-017-0260-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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74
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Bardelli A, Pantel K. Liquid Biopsies, What We Do Not Know (Yet). Cancer Cell 2017; 31:172-179. [PMID: 28196593 DOI: 10.1016/j.ccell.2017.01.002] [Citation(s) in RCA: 335] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
The inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens. Analysis of cell-free DNA and circulating tumor cells has the potential to change clinical practice by exploiting blood rather than tissue as a source of information. Liquid biopsies are already used to monitor disease response and track the emergence of drug resistance. The suitability of blood-based molecular profiles for early detection and monitoring minimal residual disease is being evaluated. In this review, we address open questions in this fast-evolving field of research.
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Affiliation(s)
- Alberto Bardelli
- University of Torino, Department of Oncology, SP 142, Km 3.95, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy.
| | - Klaus Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246 Hamburg, Germany.
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75
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Zhang W, Xia W, Lv Z, Ni C, Xin Y, Yang L. Liquid Biopsy for Cancer: Circulating Tumor Cells, Circulating Free DNA or Exosomes? Cell Physiol Biochem 2017; 41:755-768. [PMID: 28214887 DOI: 10.1159/000458736] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/08/2016] [Indexed: 01/02/2023] Open
Abstract
Precision medicine and personalized medicine are based on the development of biomarkers, and liquid biopsy has been reported to be able to detect biomarkers that carry information on tumor development and progression. Compared with traditional 'solid biopsy', which cannot always be performed to determine tumor dynamics, liquid biopsy has notable advantages in that it is a noninvasive modality that can provide diagnostic and prognostic information prior to treatment, during treatment and during progression. In this review, we describe the source, characteristics, technology for detection and current situation of circulating tumor cells, circulating free DNA and exosomes used for diagnosis, recurrence monitoring, prognosis assessment and medication planning.
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76
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Kwapisz D. The first liquid biopsy test approved. Is it a new era of mutation testing for non-small cell lung cancer? ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:46. [PMID: 28251125 DOI: 10.21037/atm.2017.01.32] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Specific mutations in epidermal growth factor receptor (EGFR) gene are predictive for response to the EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer patients (NSCLC). According to international guidelines, the molecular testing in patients with advanced NSCLC of a non-squamous subtype is recommended. However, obtain a tissue sample could be challenging. Liquid biopsy allows to determine patients suitable for EGFR-targeted therapy by analysis of circulating-free tumor DNA (cfDNA) in peripheral blood samples and might replace tissue biopsy. It allows to acquire a material in convenient minimally invasive manner, is easily repeatable, could be used for molecular identification and molecular changes monitoring. Many studies show a high concordance rate between tissue and plasma samples testing. When U.S. Food and Drug Administration (FDA) approved the first liquid biopsy test, analysis of driver gene mutation from cfDNA becomes a reality in clinical practice for patients with NSCLC.
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Affiliation(s)
- Dorota Kwapisz
- MSC Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
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77
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Yuan JQ, Zhang YL, Li HT, Mao C. EGFR mutation testing in blood for guiding EGFR tyrosine kinase inhibitor treatment in patients with nonsmall cell lung cancer: A protocol for systematic review and meta-analysis. Medicine (Baltimore) 2017; 96:e6151. [PMID: 28207548 PMCID: PMC5319537 DOI: 10.1097/md.0000000000006151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) mutation testing in tumor tissue is now a common practice in selecting non-small cell lung cancer (NSCLC) patients for EGFR tyrosine kinase inhibitor (TKI) treatment. However, tumor tissues are often absent or insufficient for the testing. Blood is a potential substitute providing a noninvasive, easily accessible and repeatedly measureable source of genotypic information. However which is the best blood EGFR mutation testing method remains unclear. We undertake this study to investigate the best blood EGFR mutation testing method for selecting EGFR TKI treatment in patients with NSCLC. METHODS This study was registered in PROSPERO (CRD42017055263). PubMed, EMBASE, Cochrane library, and NIHR Health Technology Assessment program will be searched. Studies fulfill the following criteria will be eligible: (1) randomized controlled trials or cohort studies; (2) included patients with NSCLC; (3) reported response, progression-free survival, or overall survival for EGFR TKI by the EGFR mutation status in blood sample. Diagnostic accuracy of blood EGFR mutation tests for predicting response to TKI will be pooled. Tumor response, progression-free survival, and overall survival according to different blood EGFR mutation testing methods will be evaluated and compared. RESULTS Based published data and combined analysis, this study will quantitatively compare the blood EGFR mutation testing methods according to their accuracy for predicting treatment response and relationship with clinical outcome in NSCLC patients treated with EGFR TKIs. CONCLUSION This protocol will determine the best blood EGFR mutation testing method.
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Affiliation(s)
- Jin-Qiu Yuan
- School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Yue-Lun Zhang
- School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Hai-Tao Li
- School of Medicine, Shenzhen University, Shenzhen, China
| | - Chen Mao
- School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
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78
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Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management. Int J Mol Sci 2017; 18:ijms18020264. [PMID: 28146051 PMCID: PMC5343800 DOI: 10.3390/ijms18020264] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/10/2017] [Accepted: 01/18/2017] [Indexed: 02/06/2023] Open
Abstract
Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.
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79
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Jang K, Choi J, Park C, Na S. Label-free and high-sensitive detection of Kirsten rat sarcoma viral oncogene homolog and epidermal growth factor receptor mutation using Kelvin probe force microscopy. Biosens Bioelectron 2017; 87:222-228. [DOI: 10.1016/j.bios.2016.08.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022]
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80
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Breast Cancer Genomics. Breast Cancer 2017. [DOI: 10.1007/978-3-319-48848-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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81
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Wu YL, Sequist LV, Hu CP, Feng J, Lu S, Huang Y, Li W, Hou M, Schuler M, Mok T, Yamamoto N, O'Byrne K, Hirsh V, Gibson N, Massey D, Kim M, Yang JCH. EGFR mutation detection in circulating cell-free DNA of lung adenocarcinoma patients: analysis of LUX-Lung 3 and 6. Br J Cancer 2016; 116:175-185. [PMID: 28006816 PMCID: PMC5243999 DOI: 10.1038/bjc.2016.420] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 10/17/2016] [Accepted: 11/16/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In the Phase III LUX-Lung 3/6 (LL3/LL6) trials in epidermal growth factor receptor (EGFR) mutation-positive lung adenocarcinoma patients, we evaluated feasibility of EGFR mutation detection using circulating cell-free DNA (cfDNA) and prognostic and predictive utility of cfDNA positivity (cfDNA+). METHODS Paired tumour and blood samples were prospectively collected from randomised patients. Mutations were detected using cfDNA from serum (LL3) or plasma (LL6) by a validated allele-specific quantitative real-time PCR kit. RESULTS EGFR mutation detection rates in cfDNA were 28.6% (serum) and 60.5% (plasma). Mutation detection in blood was associated with advanced disease characteristics, including higher performance score, number of metastatic sites and bone/liver metastases, and poorer prognosis. In patients with common EGFR mutations, afatinib improved progression-free survival vs chemotherapy in cfDNA+ (LL3: HR, 0.35; P=0.0009; LL6: HR, 0.25; P<0.0001) and cfDNA- (LL3: HR, 0.46; P<0.0001; LL6: HR, 0.12; P<0.0001) cohorts. A trend towards overall survival benefit with afatinib was observed in cfDNA+ patients. CONCLUSIONS Plasma cfDNA is a promising alternative to biopsy for EGFR testing. Detectable mutation in blood was associated with more advanced disease and poorer prognosis. Afatinib improved outcomes in EGFR mutation-positive patients regardless of blood mutation status.
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Affiliation(s)
- Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou 510080, China
| | - Lecia V Sequist
- Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Cheng-Ping Hu
- Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410018, China
| | - Jifeng Feng
- Jiangsu Provincial Tumor Hospital, 42 Baiziting, Xuanwu, Nanjing, Jiangsu 210009, China
| | - Shun Lu
- Shanghai Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 Huaihai West Road, Xuhui, Shanghai 200030, China
| | - Yunchao Huang
- Yunnan Tumor Hospital (The Third Affiliated Hospital of Kunming Medical University), Xingjie Alley, Xishan, Kunming, Yunnan, China
| | - Wei Li
- Cancer Center, First Hospital of Jilin University, 71 Xinmin Street, Changchun, 130021, China
| | - Mei Hou
- West China Hospital, Sichuan University, 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Martin Schuler
- West German Cancer Center, University Duisburg-Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen 45147, Germany
| | - Tony Mok
- The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Nobuyuki Yamamoto
- Wakayama Medical University, 811-1 Kimiidera, Wakayama, Wakayama Prefecture 641-8509, Japan
| | - Kenneth O'Byrne
- Princess Alexandra Hospital and Queensland University of Technology, 199 Ipswich Road, Woolloongabba, QLD 4102, Australia
| | - Vera Hirsh
- McGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, Canada
| | - Neil Gibson
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Street 65, Biberach 88400, Germany
| | - Dan Massey
- Boehringer Ingelheim Ltd UK, Ellesfield Avenue, Bracknell, Berkshire RG12 8YS, UK
| | - Miyoung Kim
- Boehringer Ingelheim GmbH, Binger Street 173, Ingelheim 55216, Germany
| | - James Chih-Hsin Yang
- National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei 100, Taiwan
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82
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Wang W, Song Z, Zhang Y. A Comparison of ddPCR and ARMS for detecting EGFR T790M status in ctDNA from advanced NSCLC patients with acquired EGFR-TKI resistance. Cancer Med 2016; 6:154-162. [PMID: 28000387 PMCID: PMC5269560 DOI: 10.1002/cam4.978] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/13/2016] [Accepted: 10/29/2016] [Indexed: 12/16/2022] Open
Abstract
A sensitive and convenient method for detecting epidermal growth factor receptor (EGFR) T790M mutations from circulating tumor DNA (ctDNA) in advanced non–small cell lung cancer (NSCLC) patients with acquired EGFR‐TKI resistance would be desirable to direct patient sequential treatment strategy. A comparison of two platforms for detecting EGFR mutations in plasma ctDNA was undertaken. Plasma samples and tumor samples were collected from patients with acquired EGFR‐TKI resistance in Zhejiang Cancer Hospital from December 2014 to December 2015. Extracted ctDNA was analyzed using two platforms (Droplet Digital PCR and ARMS [dPCR]). A total of 108 patients were enrolled in this study. One hundred and eight patient plasma samples were detected by ddPCR and 75 were detected by ARMS. And 16 patients obtained tissue re‐biopsy, using ARMS assay for detecting EGFR T790M mutation. In all, 43.7% (47/108) had acquired T790M mutation by ddPCR. In 75 patient plasma samples, comparing ddPCR with ARMS, the rates of T790M mutation were 46.7% (35/75) and 25.3% (19/75) by ddPCR and ARMS, respectively. Of all, 16 patients both had tumor and plasma samples, the T790M mutation rates were 56.3% (9/16) by ARMS in tissue and 50.5% (8/16) by ddPCR in plasma ctDNA. The progression mode tended to gradual progression in T790M mutation patients (40.4%), but the T790M negative was inclined to the mode of dramatic progression (39.3%). The patients with T790M‐positive tumors had a longer time to disease progression after treatment with EGFR‐TKIs (median, 13.1 months vs. 10.8 months; P = 0.010) and overall survival (median, 35.3 months vs. 30.3 months; P = 0.214) compared with those with T790M‐negative patients. Our study demonstrates ddPCR assay may provide a highly sensitive method to detect EGFR T790M gene in plasma. And T790M‐positive patients have better clinical outcomes to EGFR‐TKIs than T790M‐negative patients.
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Affiliation(s)
- Wenxian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zhengbo Song
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Yiping Zhang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China.,Key Laboratory Diagnosis and Treatment Technology on Thoracic Oncology, Zhejiang, China
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83
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Wu TH, Hsiue EHC, Lee JH, Lin CC, Yang JCH. New data on clinical decisions in NSCLC patients with uncommon EGFR mutations. Expert Rev Respir Med 2016; 11:51-55. [DOI: 10.1080/17476348.2017.1267569] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ting-Hui Wu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Jih-Hsiang Lee
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Chi Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- National Taiwan University Cancer Center, Taipei, Taiwan
| | - James Chih-Hsin Yang
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- National Taiwan University Cancer Center, Taipei, Taiwan
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84
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Pérez-Barrios C, Nieto-Alcolado I, Torrente M, Jiménez-Sánchez C, Calvo V, Gutierrez-Sanz L, Palka M, Donoso-Navarro E, Provencio M, Romero A. Comparison of methods for circulating cell-free DNA isolation using blood from cancer patients: impact on biomarker testing. Transl Lung Cancer Res 2016; 5:665-672. [PMID: 28149760 DOI: 10.21037/tlcr.2016.12.03] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND The implementation of liquid biopsy for biomarker testing and response to treatment monitoring in cancer patients would presumable increase laboratory throughput, requiring the development of automated methods for circulating free DNA (cfDNA) isolation. METHODS The present study compares the MagNA Pure Compact (MPC) Nucleic Acid Isolation Kit I and Maxwell® RSC (MR) ccfDNA Plasma Kit and the later with QIAamp Circulating Nucleid Acid (QCNA) Kit using 57 plasma samples from cancer patients. cfDNA concentration was measured using the Qubit fluorometer. DNA fragments lengt were assessed using the Agilent 2100 Bioanalyzer. Circulating tumor DNA (ctDNA) was quantified by digital PCR (dPCR). RESULTS Firstly, we observed that MPC method significantly extracted less cfDNA than MR (P<0.0001). However, there were no significant differences in extraction yields of QCNA and MR kits. cfDNA isolation yield was also associated with tumor stage but not with tumor location. Secondly, an oligonucleosomal DNA ladder pattern was observed in 88% of the samples and significant differences in the recovery of mono-, di- and tri-nucleosomes DNA fragments were observed between MPC and MR methodologies. Finally, tumor mutation quantification on cfDNA was performed on 38 paired samples using digital PCR. Mutant allele fractions (MAFs) between paired samples were not significantly different. CONCLUSIONS Methods for isolation of cfDNA can affect DNA yield and molecular weight fractions recovery. These observations should be taken into account for cfDNA analysis in routine clinical practice.
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Affiliation(s)
| | | | - María Torrente
- Medical Oncology Department, Puerta de Hierro Hospital, Madrid, Spain
| | | | - Virginia Calvo
- Medical Oncology Department, Puerta de Hierro Hospital, Madrid, Spain
| | | | - Magda Palka
- Medical Oncology Department, Puerta de Hierro Hospital, Madrid, Spain
| | | | - Mariano Provencio
- Medical Oncology Department, Puerta de Hierro Hospital, Madrid, Spain
| | - Atocha Romero
- Traslational Oncology Laboratoryt, Puerta de Hierro Hospital, Madrid, Spain; Medical Oncology Department, Puerta de Hierro Hospital, Madrid, Spain
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85
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Xiao Z, Song Y, Wang K, Sun X, Shen B. One-step radiosynthesis of 18F-IRS: A novel radiotracer targeting mutant EGFR in NSCLC for PET/CT imaging. Bioorg Med Chem Lett 2016; 26:5985-5988. [PMID: 27825546 DOI: 10.1016/j.bmcl.2016.10.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
EGFR (epidermal growth factor receptor) targeted therapy has shown great success in clinical comparing with chemotherapy in EGFR mutation NSCLCs. Such as, gefitinib, first generation EGFR TKI, has obviously prolonged the FPS (progression free survival) of the subgroup of patients, but to those who did not get a certain mutation in EGFR kinase domain, the outcome is poor. In view of this situation, scientists have synthesized many radiotracers for selecting the right people by PET/CT imaging to NSCLC TKI therapy. In this study, we developed a novel PET radiotracer 18F-IRS in one-step with a radio yield 20% (non-corrected), radiochemistry>98.5%, specific activity>105GBq/μmol, the pharmacokinetics and capacity of the tracer binding to mutant EGFR were evaluated both in vitro and in vivo.
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Affiliation(s)
- Zunyu Xiao
- TOF-PET/CT/MR Center, The Fourth Hospital of Harbin Medical University, China; Molecular Imaging Research Center, Harbin Medical University, China
| | - Yan Song
- TOF-PET/CT/MR Center, The Fourth Hospital of Harbin Medical University, China; Molecular Imaging Research Center, Harbin Medical University, China
| | - Kai Wang
- TOF-PET/CT/MR Center, The Fourth Hospital of Harbin Medical University, China; Molecular Imaging Research Center, Harbin Medical University, China
| | - Xilin Sun
- TOF-PET/CT/MR Center, The Fourth Hospital of Harbin Medical University, China; Molecular Imaging Research Center, Harbin Medical University, China.
| | - Baozhong Shen
- TOF-PET/CT/MR Center, The Fourth Hospital of Harbin Medical University, China; Molecular Imaging Research Center, Harbin Medical University, China.
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86
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Pérez-Callejo D, Romero A, Provencio M, Torrente M. Liquid biopsy based biomarkers in non-small cell lung cancer for diagnosis and treatment monitoring. Transl Lung Cancer Res 2016; 5:455-465. [PMID: 27826527 DOI: 10.21037/tlcr.2016.10.07] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Advances in the knowledge of the biology of non-small cell lung cancer (NSCLC) 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. Moreover, a single biopsy cannot reflect the clonal heterogeneity of the tumor. The analysis of peripheral blood samples of cancer patients represents a new source of cancer-derived material, known as liquid biopsy, and its components can be obtained from almost all 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. The present review focuses on the liquid biopsy components: circulating tumor cells (CTCS), circulating free DNA (cfDNA), exosomes and tumor-educated platelets (TEP); the isolation technologies used and their potential use for non-invasive screening, early diagnosis, prognosis, response to treatment and real time monitoring of the disease, in NSCLC patients.
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Affiliation(s)
- David Pérez-Callejo
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Atocha Romero
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Mariano Provencio
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - María Torrente
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
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87
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Xu S, Duan Y, Lou L, Tang F, Shou J, Wang G. Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncol Lett 2016; 12:4238-4244. [PMID: 27895798 DOI: 10.3892/ol.2016.5184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/05/2016] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to explore the influence of T790M neighboring single nucleotide polymorphism (SNP) on the sensitivity of amplification refractory mutation system (ARMS)-based T790M mutation assay. Three ARMS-quantitative polymerase chain reaction (qPCR) systems (system 1 had a forward ARMS primer without rs1050171, system 2 included a forward ARMS primer with rs1050171 and system 3 contained the above two forward ARMS primers) were used to detect the T790M mutation in two series plasmid samples and genomic DNA (gDNA) of the cell line H1975. A total of 670 formalin-fixed paraffin-embedded (FFPE) tumor samples from non-small cell lung cancer patients were used to detect the epidermal growth factor receptor (EGFR) gene T790M mutation by direct sequencing and ARMS-qPCR. The ARMS-qPCR system 1 effectively detected samples with as low as 1% T790M mutant plasmid 1 (without rs1050171) and with 50% T790M mutant plasmid 2 (with rs1050171), while the ARMS-qPCR system 2 detected samples with 20 and 50% T790M mutant plasmid 1, in addition to samples with 1% T790M mutant plasmid 2. For the ARMS-qPCR system 3, samples with as low as 1% T790M mutant plasmids 1 or 2 were effectively detected. For gDNA analysis of the cell line H1975, the T790M mutation was effectively detected by the ARMS-qPCR systems 2 and 3 (~50% mutation rate), but was detected with a low mutation abundance by the ARMS-qPCR system 1 (~1% mutation rate). Of the 670 FFPE samples, 5 cases were identified to have the T790M mutation by sequencing and by the ARMS-qPCR system 1. One sample (named N067), which was considered as T790M-negative by sequencing, was demonstrated to have the T790M mutation using the ARMS-qPCR system 1. Sample N094, which was variant homozygous for rs1050171 and was indicated to be T790M-negative by sequencing and by the ARMS-qPCR system 1, was identified to have the T790M mutation with the ARMS-qPCR system 3. The A-variant allele frequency of rs1050171 was observed to be 28.2% in the 670 FFPE tumor samples, while the presence of rs148188503 (c. C2355T, p. T785T) was observed in sample N558, and a novel SNP with a base substitution (c. T2375C) at position 792 (p. L792P) in exon 20 of the EGFR gene was observed in sample N310. rs1050171 is a high-frequency SNP located near T790M, and the mutation statuses of rs1050171 appear to influence the sensitivity of the ARMS-based T790M detection system, thus generating a 14.3% false-negative rate (1/7). The present study proposes the risk that target neighboring SNPs (as far as 8 bp away in the present study) may exert on the sensitivity of ARMS-based detection methods.
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Affiliation(s)
- Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liping Lou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Fengjuan Tang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Juan Shou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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88
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Thompson JC, Yee SS, Troxel AB, Savitch SL, Fan R, Balli D, Lieberman DB, Morrissette JD, Evans TL, Bauml J, Aggarwal C, Kosteva JA, Alley E, Ciunci C, Cohen RB, Bagley S, Stonehouse-Lee S, Sherry VE, Gilbert E, Langer C, Vachani A, Carpenter EL. Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA. Clin Cancer Res 2016; 22:5772-5782. [PMID: 27601595 DOI: 10.1158/1078-0432.ccr-16-1231] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE The expanding number of targeted therapeutics for non-small cell lung cancer (NSCLC) necessitates real-time tumor genotyping, yet tissue biopsies are difficult to perform serially and often yield inadequate DNA for next-generation sequencing (NGS). We evaluated the feasibility of using cell-free circulating tumor DNA (ctDNA) NGS as a complement or alternative to tissue NGS. EXPERIMENTAL DESIGN A total of 112 plasma samples obtained from a consecutive study of 102 prospectively enrolled patients with advanced NSCLC were subjected to ultra-deep sequencing of up to 70 genes and matched with tissue samples, when possible. RESULTS We detected 275 alterations in 45 genes, and at least one alteration in the ctDNA for 86 of 102 patients (84%), with EGFR variants being most common. ctDNA NGS detected 50 driver and 12 resistance mutations, and mutations in 22 additional genes for which experimental therapies, including clinical trials, are available. Although ctDNA NGS was completed for 102 consecutive patients, tissue sequencing was only successful for 50 patients (49%). Actionable EGFR mutations were detected in 24 tissue and 19 ctDNA samples, yielding concordance of 79%, with a shorter time interval between tissue and blood collection associated with increased concordance (P = 0.038). ctDNA sequencing identified eight patients harboring a resistance mutation who developed progressive disease while on targeted therapy, and for whom tissue sequencing was not possible. CONCLUSIONS Therapeutically targetable driver and resistance mutations can be detected by ctDNA NGS, even when tissue is unavailable, thus allowing more accurate diagnosis, improved patient management, and serial sampling to monitor disease progression and clonal evolution. Clin Cancer Res; 22(23); 5772-82. ©2016 AACR.
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Affiliation(s)
- Jeffrey C Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Andrea B Troxel
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Samantha L Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - David Balli
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David B Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer D Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tracey L Evans
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Joshua Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - John A Kosteva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Evan Alley
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christine Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Roger B Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephen Bagley
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Susan Stonehouse-Lee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Victoria E Sherry
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Elizabeth Gilbert
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Corey Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Anil Vachani
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. .,Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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89
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Nakahara Y, Takagi Y, Hosomi Y, Kagei A, Yamamoto T, Sawada T, Yomota M, Okuma Y, Mikura S, Okamura T. Noninvasive monitoring of the genetic evolution of EGFR-mutant non-small-cell lung cancer by analyzing circulating tumor DNA during combination chemotherapy with gefitinib and pemetrexed or S-1. Onco Targets Ther 2016; 9:5287-95. [PMID: 27601920 PMCID: PMC5004997 DOI: 10.2147/ott.s105976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Repetitive genotyping is useful to assess the genetic evolution of non-small-cell lung cancer (NSCLC) during treatment, but the need for sampling by biopsy is a major obstacle. Digital polymerase chain reaction (PCR) is a promising procedure for the detection of mutant alleles in plasma of cancer patients. Methods This prospective study enrolled patients with NSCLC and known epidermal growth factor receptor (EGFR) mutations and who had experienced disease progression during ongoing EGFR-tyrosine kinase inhibitor (TKI) therapy. Eligible patients received daily gefitinib and either pemetrexed or S-1 every 3 weeks until disease progression or the development of unacceptable toxicity. Peripheral blood was collected before and after the combination therapy for digital PCR and hepatocyte growth factor measurement. Results From May 2012 to January 2014, nine patients with a median age of 67 (range 52–80) years were enrolled. Patterns of disease progression during adjacent EGFR-TKI therapy were acquired resistance, observed in seven patients, and primary resistance, observed in two patients. Known EGFR mutations were detected in plasma samples of six (67%) patients at study enrollment. Of these, T790M mutation was concurrently detected in three (50%) patients. Four patients underwent gefitinib plus pemetrexed therapy, and five patients underwent gefitinib and S-1 therapy. The median number of cycles delivered was five, and the median progression-free survival was 5.7 months. Efficacy outcomes did not differ between treatments. After the combination therapy, plasma T790M status changed to positive in two patients. Hepatocyte growth factor level did not significantly change through the combination therapy. Conclusion The usefulness of monitoring the genetic evolution of EGFR-driven tumors using noninvasive procedures was demonstrated. Since continuation of EGFR-TKI therapy with cytotoxic agents has an acceptable tolerability and a possibility of inducing T790M mutation, the combination therapy may be useful for EGFR-mutant NSCLC resistant to EGFR-TKI therapy without T790M mutation.
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Affiliation(s)
- Yoshiro Nakahara
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo; Department of Respiratory Medicine, Kitasato University School of Medicine, Sagamihara
| | - Yusuke Takagi
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo; Oncology Scientific Affairs, Merck Sharp & Dohme Corp
| | - Yukio Hosomi
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo
| | | | | | - Takeshi Sawada
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo
| | - Makiko Yomota
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo
| | - Yusuke Okuma
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo
| | - Shinichiro Mikura
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo; Department of Respiratory Medicine, Fujieda Municipal General Hospital, Fujieda, Japan
| | - Tatsuru Okamura
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo
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90
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Ishii H, Azuma K, Sakai K, Kawahara A, Yamada K, Tokito T, Okamoto I, Nishio K, Hoshino T. Digital PCR analysis of plasma cell-free DNA for non-invasive detection of drug resistance mechanisms in EGFR mutant NSCLC: Correlation with paired tumor samples. Oncotarget 2016; 6:30850-8. [PMID: 26334838 PMCID: PMC4741572 DOI: 10.18632/oncotarget.5068] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/04/2015] [Indexed: 01/10/2023] Open
Abstract
As the development of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) has become an issue of concern, identification of the mechanisms responsible has become an urgent priority. However, for research purposes, it is not easy to obtain tumor samples from patients with EGFR mutation-positive non-small-cell lung cancer (NSCLC) that has relapsed after treatment with EGFR-TKIs. Here, using digital PCR assay as an alternative and noninvasive method, we examined plasma and tumor samples from patients with relapsed NSCLC to establish the inter-relationships existing among T790M mutation, activating EGFR mutations, HER2 amplification, and MET amplification. Paired samples of tumor and blood were obtained from a total of 18 patients with NSCLC after they had developed resistance to EGFR-TKI treatment, and the mechanisms of resistance were analyzed by digital PCR. Digital PCR analysis of T790M mutation in plasma had a sensitivity of 81.8% and specificity of 85.7%, the overall concordance between plasma and tissue samples being 83.3%. MET gene copy number gain in tumor DNA was observed by digital PCR in three patients, of whom one exhibited positivity for MET amplification by FISH, whereas no patient demonstrated MET and HER2 copy number gain in plasma DNA. Digital PCR analysis of plasma is feasible and accurate for detection of T790M mutation in NSCLC that becomes resistant to treatment with EGFR-TKIs.
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Affiliation(s)
- Hidenobu Ishii
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Koichi Azuma
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Akihiko Kawahara
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Fukuoka, Japan
| | - Kazuhiko Yamada
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Takaaki Tokito
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Isamu Okamoto
- Center for Clinical and Translational Research, Kyusyu University Hospital, Fukuoka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka, Japan
| | - Tomoaki Hoshino
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
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91
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Levy B, Hu ZI, Cordova KN, Close S, Lee K, Becker D. Clinical Utility of Liquid Diagnostic Platforms in Non-Small Cell Lung Cancer. Oncologist 2016; 21:1121-30. [PMID: 27388233 DOI: 10.1634/theoncologist.2016-0082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 11/17/2022] Open
Abstract
UNLABELLED : A firmer understanding of the genomic landscape of lung cancer has recently led to targeted, therapeutic advances in non-small cell lung cancer. Historically, the reference standard for the diagnosis and genetic interrogation for advanced-stage patients has been tissue acquisition via computed tomography-guided core or fine needle aspiration biopsy. However, this process can frequently put the patient at risk and remains complicated by sample availability and tumor heterogeneity. In addition, the time required to complete the diagnostic assays can negatively affect clinical care. Technological advances in recent years have led to the development of blood-based diagnostics or "liquid biopsies" with great potential to quickly diagnose and genotype lung cancer using a minimally invasive technique. Recent studies have suggested that molecular alterations identified in cell-free DNA (cfDNA) or circulating tumor DNA can serve as an accurate molecular proxy of tumor biology and reliably predict the response to tyrosine kinase therapy. In addition, several trials have demonstrated the high accuracy of microRNA (miRNA) platforms in discerning cancerous versus benign nodules in high-risk, screened patients. Despite the promise of these platforms, issues remain, including varying sensitivities and specificities between competing platforms and a lack of standardization of techniques and downstream processing. In the present report, the clinical applications of liquid biopsy technologies, including circulating tumor cells, proteomics, miRNA, and cfDNA for NSCLC, are reviewed and insight is provided into the diagnostic and therapeutic implications and challenges of these platforms. IMPLICATIONS FOR PRACTICE Although tumor biopsies remain the reference standard for the diagnosis and genotyping of non-small cell lung cancer, they remain fraught with logistical complexities that can delay treatment decisions and affect clinical care. Liquid diagnostic platforms, including cell-free DNA, proteomic signatures, RNA (mRNA and microRNA), and circulating tumor cells, have the potential to overcome many of these barriers, including rapid and accurate identification of de novo and resistant genetic alterations, real-time monitoring of treatment responses, prognosis of outcomes, and identification of minimal residual disease. The present report provides insights into new liquid diagnostic platforms in non-small cell lung cancer and discusses the promise and challenges of their current and future clinical use.
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Affiliation(s)
- Benjamin Levy
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Zishuo I Hu
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | | | | | - Karen Lee
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Daniel Becker
- Veterans Affairs Hospital, New York University, New York, New York, USA
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92
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Zheng D, Chen H. [Advances in Liquid Biopsy and its Clinical Application in the Diagnosis
and Treatment of Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2016; 19:394-8. [PMID: 27335304 PMCID: PMC6015208 DOI: 10.3779/j.issn.1009-3419.2016.06.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
随着近几年科学技术的进步,液体活检技术也有了长足的发展,并在肿瘤的早期诊断及后期治疗中扮演着越来越重要的角色。相比于传统的组织活检,液体活检以其独有的无创性、便捷性、高重复性等特点在临床上得到更多的青睐,在未来有着巨大的发展潜力。本文重点探讨了循环肿瘤细胞(circulating tumor cells, CTCs)和循环肿瘤DNA(circulating tumor DNA, ctDNA),作为液体活检最重要的两个检测对象,其历史、生物学特性,检测手段,局限性及其在非小细胞肺癌诊治中的应用。
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Affiliation(s)
- Difan Zheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
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93
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Karlovich C, Goldman JW, Sun JM, Mann E, Sequist LV, Konopa K, Wen W, Angenendt P, Horn L, Spigel D, Soria JC, Solomon B, Camidge DR, Gadgeel S, Paweletz C, Wu L, Chien S, O’Donnell P, Matheny S, Despain D, Rolfe L, Raponi M, Allen AR, Park K, Wakelee H. Assessment of EGFR Mutation Status in Matched Plasma and Tumor Tissue of NSCLC Patients from a Phase I Study of Rociletinib (CO-1686). Clin Cancer Res 2016; 22:2386-95. [PMID: 26747242 PMCID: PMC6886231 DOI: 10.1158/1078-0432.ccr-15-1260] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022]
Abstract
PURPOSE The evaluation of plasma testing for the EGFR resistance mutation T790M in NSCLC patients has not been broadly explored. We investigated the detection of EGFR activating and T790M mutations in matched tumor tissue and plasma, mostly from patients with acquired resistance to first-generation EGFR inhibitors. EXPERIMENTAL DESIGN Samples were obtained from two studies, an observational study and a phase I trial of rociletinib, a mutant-selective inhibitor of EGFR that targets both activating mutations and T790M. Plasma testing was performed with the cobas EGFR plasma test and BEAMing. RESULTS The positive percent agreement (PPA) between cobas plasma and tumor results was 73% (55/75) for activating mutations and 64% (21/33) for T790M. The PPA between BEAMing plasma and tumor results was 82% (49/60) for activating mutations and 73% (33/45) for T790M. Presence of extrathoracic (M1b) versus intrathoracic (M1a/M0) disease was found to be strongly associated with ability to identify EGFR mutations in plasma (P < 0.001). Rociletinib objective response rates (ORR) were 52% [95% confidence interval (CI), 31 - 74%] for cobas tumor T790M-positive and 44% (95% CI, 25 - 63%) for BEAMing plasma T790M-positive patients. A drop in plasma-mutant EGFR levels to ≤10 molecules/mL was seen by day 21 of treatment in 7 of 8 patients with documented partial response. CONCLUSIONS These findings suggest the cobas and BEAMing plasma tests can be useful tools for noninvasive assessment and monitoring of the T790M resistance mutation in NSCLC, and could complement tumor testing by identifying T790M mutations missed because of tumor heterogeneity or biopsy inadequacy. Clin Cancer Res; 22(10); 2386-95. ©2016 AACR.
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Affiliation(s)
| | | | - Jong-Mu Sun
- Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Elaina Mann
- Clovis Oncology Inc., San Francisco, California
| | | | | | - Wei Wen
- Roche Molecular Systems, Pleasanton, California
| | | | - Leora Horn
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - David Spigel
- Sarah Cannon Research Institute, Nashville; Tennessee
| | | | | | | | - Shirish Gadgeel
- Karmanos Cancer Institute/Wayne State University, Detroit, Michigan
| | | | - Lin Wu
- Roche Molecular Systems, Pleasanton, California
| | - Sean Chien
- Roche Molecular Systems, Pleasanton, California
| | | | | | | | | | | | | | - Keunchil Park
- Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, Korea
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94
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ZHAO JING, FENG HUAHUA, ZHAO JINYIN, LIU LICHENG, XIE FEIFEI, XU YAN, CHEN MINJIANG, ZHONG WEI, LI LONGYUN, WANG HANPING, ZHANG LI, XIAO YI, CHEN WEIJUN, WANG MENGZHAO. A sensitive and practical method to detect the T790M mutation in the epidermal growth factor receptor. Oncol Lett 2016; 11:2573-2579. [PMID: 27073519 PMCID: PMC4812525 DOI: 10.3892/ol.2016.4263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 02/08/2016] [Indexed: 12/17/2022] Open
Abstract
The current study aimed to develop a method to rapidly, sensitively and practically screen for the epidermal growth factor receptor (EGFR) T790M mutation. This method combines an allele-specific competitive blocker (ACB) with a TaqMan quantitative polymerase chain reaction (PCR) amplification refractory mutation system (ARMS) in a one-step reaction. Using a mimic of a human genomic DNA panel containing serially diluted mutant alleles, the performance efficacy of this method was assessed. Using this method, the EGFR T790M mutation was detected in tyrosine kinase inhibitor (TKI)-naïve samples obtained from 27 non-small cell lung cancer (NSCLC) patients with EGFR-activating mutations. The association between de novo T790M mutations and the clinical benefit of EGFR-TKI treatment was also analysed. The sensitivity of this method was as low as 0.01%. In the samples from the 27 NSCLC patients, this method identified 6 mutant patients (22.2%), which was higher than the detection rate with scorpion ARMS (0.0%). No clinical variables were associated with the occurrence of a de novo T790M mutation. The median progression-free survival time in the TKI-naïve patients with a T790M mutation was shorter that that of patients without the mutation, but the difference was not significant (3.2 vs. 19.5 months, respectively; P=0.256). The median overall survival time in the groups with or without T790M mutation also did not significantly differ (10 vs. 20 months, respectively; P=0.689). Overall, the ACB-ARMS PCR method could be useful for detecting the EGFR T790M mutation in clinical samples that contain only a small number of mutant alleles. The clinical significance of a de novo T790M mutation should be further investigated.
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Affiliation(s)
- JING ZHAO
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - HUA-HUA FENG
- Beijing BGI-GBI Biotech Co., Ltd., Beijing 101300, P.R. China
| | - JIN-YIN ZHAO
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - LI-CHENG LIU
- Beijing BGI-GBI Biotech Co., Ltd., Beijing 101300, P.R. China
| | - FEI-FEI XIE
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - YAN XU
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - MIN-JIANG CHEN
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - WEI ZHONG
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - LONG-YUN LI
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - HAN-PING WANG
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - LI ZHANG
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - YI XIAO
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - WEI-JUN CHEN
- Beijing BGI-GBI Biotech Co., Ltd., Beijing 101300, P.R. China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - MENG-ZHAO WANG
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
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95
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Plasma EGFR T790M ctDNA status is associated with clinical outcome in advanced NSCLC patients with acquired EGFR-TKI resistance. Sci Rep 2016; 6:20913. [PMID: 26867973 PMCID: PMC4751431 DOI: 10.1038/srep20913] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/13/2016] [Indexed: 01/03/2023] Open
Abstract
EGFR T790M mutation occurs in half of non-small cell lung cancer (NSCLC) patients with acquired EGFR-TKI (TKI) resistance, based on tumor re-biopsies using an invasive clinical procedure. Here, we dynamically monitored T790M mutation in circulating tumor DNA (ctDNA) using serial plasma samples from NSCLC patients receiving TKI through Droplet Digital PCR (ddPCR) method and the associations between overall survival (OS) starting from initial TKI treatment and the T790M ctDNA status detected in plasma were analyzed. Among 318 patients, 117 who acquired TKI resistance were eligible for the analysis. T790M ctDNA was detected in the plasma of 55/117 (47%) patients. Almost half of the T790M ctDNA positive patients were identified at a median time of 2.2 months prior to clinically progressive disease (PD). Furthermore, within the patients receiving TKI treatment at 2(nd) line or later, the T790M ctDNA positive group had significantly shorter OS than the negative group (median OS: 26.9 months versus NA, P = 0.0489). Our study demonstrates the feasibility of monitoring EGFR mutation dynamics in serial plasma samples from NSCLC patients receiving TKI therapy. T790M ctDNA can be detected in plasma before and after PD as a poor prognostic factor.
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96
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Tissot C, Villar S, Olivier M, Couraud S. [Free circulating DNA as a tool for lung cancer patients management]. REVUE DE PNEUMOLOGIE CLINIQUE 2016; 72:61-71. [PMID: 26190335 DOI: 10.1016/j.pneumo.2015.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 04/10/2015] [Accepted: 05/02/2015] [Indexed: 06/04/2023]
Abstract
Free circulating DNA (cfDNA) has been known for several decades. These small DNA fragments are released into the circulation from nucleated cells through necrosis, apoptosis and/or active secretion. These genomic fragments are mainly constitutional (nucleated blood cell DNA), but in patients with cancer, a fraction comes from tumor cells. Although poorly known in the field of thoracic oncology, quantitative and qualitative analysis of the cDNA is nevertheless of great interest. Total cfDNA concentration appears to be an independent prognostic factor in lung cancer. Although changes in total cfDNA concentration is not informative to assess the effectiveness of chemotherapy, following-up the fraction of mutated genes such as EGFR during therapy with tyrosine kinase inhibitors appears to be particularly promising for the early detection of disease progression. The use of cfDNA as liquid biopsy is also very promising for the non-invasive somatic molecular profile either at baseline either for sampling at follow-up. Thus, cfDNA is a very promising tool in thoracic oncology and its translation into practice should be developed quickly.
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Affiliation(s)
- C Tissot
- Groupe mécanismes moléculaires et biomarqueurs, Centre international de recherche sur le cancer (CIRC/IARC), 150, cours Albert-Thomas, 69372 Lyon cedex 08, France; Service de pneumologie aiguë spécialisée et cancérologie thoracique, centre hospitalier Lyon-Sud, hospices civils de Lyon, 165, chemin du Grand-Revoyet, 69495 Pierre-Bénite, France
| | - S Villar
- Groupe mécanismes moléculaires et biomarqueurs, Centre international de recherche sur le cancer (CIRC/IARC), 150, cours Albert-Thomas, 69372 Lyon cedex 08, France
| | - M Olivier
- Groupe mécanismes moléculaires et biomarqueurs, Centre international de recherche sur le cancer (CIRC/IARC), 150, cours Albert-Thomas, 69372 Lyon cedex 08, France
| | - S Couraud
- Service de pneumologie aiguë spécialisée et cancérologie thoracique, centre hospitalier Lyon-Sud, hospices civils de Lyon, 165, chemin du Grand-Revoyet, 69495 Pierre-Bénite, France; EMR 3738 ciblage thérapeutique en oncologie, faculté de médecine et de maïeutique Lyon-Sud - Charles-Mérieux, université Lyon-1, chemin de Montmein, 69600 Oullins, France.
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97
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Tsui DWY, Berger MF. Profiling Non-Small Cell Lung Cancer: From Tumor to Blood. Clin Cancer Res 2015; 22:790-2. [PMID: 26671996 DOI: 10.1158/1078-0432.ccr-15-2514] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 11/11/2015] [Indexed: 11/16/2022]
Abstract
Circulating cell-free tumor DNA has shown great promise for noninvasive genomic profiling to guide the administration of targeted therapies in non-small cell lung cancer. With advancements in molecular technology, it is now possible to interrogate multiple clinically actionable genetic drivers in the blood with a single assay.
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Affiliation(s)
- Dana W Y Tsui
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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98
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Tan CS, Gilligan D, Pacey S. Treatment approaches for EGFR-inhibitor-resistant patients with non-small-cell lung cancer. Lancet Oncol 2015; 16:e447-e459. [PMID: 26370354 DOI: 10.1016/s1470-2045(15)00246-6] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 12/13/2022]
Abstract
Discovery of activating mutations in EGFR and their use as predictive biomarkers to tailor patient therapy with EGFR tyrosine kinase inhibitors (TKIs) has revolutionised treatment of patients with advanced EGFR-mutant non-small-cell lung cancer (NSCLC). At present, first-line treatment with EGFR TKIs (gefitinib, erlotinib, and afatinib) has been approved for patients harbouring exon 19 deletions or exon 21 (Leu858Arg) substitution EGFR mutations. These agents improve response rates, time to progression, and overall survival. Unfortunately, patients develop resistance, limiting patient benefit and posing a challenge to oncologists. Optimum treatment after progression is not clearly defined. A more detailed understanding of the biology of EGFR-mutant NSCLC and the mechanisms of resistance to targeted therapy mean that an era of treatment approaches based on rationally developed drugs or therapeutic strategies has begun. Combination approaches-eg, dual EGFR blockade-to overcome resistance have been trialled and seem to be promising but are potentially limited by toxicity. Third-generation EGFR-mutant-selective TKIs, such as AZD9291 or rociletininb, which target Thr790Met-mutant tumours, the most common mechanism of EGFR TKI resistance, have entered clinical trials, and exciting, albeit preliminary, efficacy data have been reported. In this Review, we summarise the scientific literature and evidence on therapy options after EGFR TKI treatment for patients with NSCLC, aiming to provide a guide to oncologists, and consider how to maximise therapeutic advances in outcomes in this rapidly advancing area.
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Affiliation(s)
- Chee-Seng Tan
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore
| | | | - Simon Pacey
- Department of Oncology, University of Cambridge, Cambridge, UK.
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99
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Ross K, Pailler E, Faugeroux V, Taylor M, Oulhen M, Auger N, Planchard D, Soria JC, Lindsay CR, Besse B, Vielh P, Farace F. The potential diagnostic power of circulating tumor cell analysis for non-small-cell lung cancer. Expert Rev Mol Diagn 2015; 15:1605-29. [PMID: 26564313 DOI: 10.1586/14737159.2015.1111139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In non-small-cell lung cancer (NSCLC), genotyping tumor biopsies for targetable somatic alterations has become routine practice. However, serial biopsies have limitations: they may be technically difficult or impossible and could incur serious risks to patients. Circulating tumor cells (CTCs) offer an alternative source for tumor analysis that is easily accessible and presents the potential to identify predictive biomarkers to tailor therapies on a personalized basis. Examined here is our current knowledge of CTC detection and characterization in NSCLC and their potential role in EGFR-mutant, ALK-rearranged and ROS1-rearranged patients. This is followed by discussion of the ongoing issues such as the question of CTC partnership as diagnostic tools in NSCLC.
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Affiliation(s)
- Kirsty Ross
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
| | - Emma Pailler
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
| | - Vincent Faugeroux
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
| | - Melissa Taylor
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France
| | - Marianne Oulhen
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
| | - Nathalie Auger
- c Department of Biopathology , Gustave Roussy , Villejuif , France
| | - David Planchard
- d Department of Medicine , Gustave Roussy, F-94805 , Villejuif , France
| | - Jean-Charles Soria
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,d Department of Medicine , Gustave Roussy, F-94805 , Villejuif , France
| | - Colin R Lindsay
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
| | - Benjamin Besse
- d Department of Medicine , Gustave Roussy, F-94805 , Villejuif , France
| | - Philippe Vielh
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France.,c Department of Biopathology , Gustave Roussy , Villejuif , France
| | - Françoise Farace
- a INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment" , F-94805 , VILLEJUIF , France.,b Gustave Roussy, Université Paris-Saclay , "Circulating Tumor Cells" Translational Platform, CNRS UMS3655 - INSERM US23 AMMICA, F-94805 , VILLEJUIF , France
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100
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Guo K, Zhang Z, Han L, Han J, Wang J, Zhou Y, Liu H, Tong L, Li X, Yan X. Detection of epidermal growth factor receptor mutation in plasma as a biomarker in Chinese patients with early-stage non-small cell lung cancer. Onco Targets Ther 2015; 8:3289-96. [PMID: 26609241 PMCID: PMC4644181 DOI: 10.2147/ott.s94297] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose This preplanned exploratory analysis was conducted to reveal the true status of correlation between tissue and plasma detection for early-stage non-small cell lung cancer (NSCLC) epidermal growth factor receptor (EGFR) mutations, knowing that specific subgroups of NSCLC patients may be potential candidates for EGFR mutation analysis by using plasma samples. Materials and methods Tissue samples were surgically resected from 198 patients with stage I–IV NSCLC, where stage IA to IIIA accounted for 92.4%. EGFR mutations in all these tissues were positive. Paired plasma EGFR mutations were detected by real-time polymerase chain reaction; concentration of cell-free DNA (cfDNA) in plasma was measured by ultraviolet spectrophotometry. Results EGFR-activating mutation was detected in 34 plasma samples, and their mutation types were matched with that in tissue. The sensitivity of EGFR mutation for the 198 paired tissue and plasma samples was 17.2%. The sensitivity positively correlated with disease stage and negatively correlated with tumor differentiation. The sensitivity of stage IA, IB, IIA, IIB, and IIIA was 1.6%, 7.9%, 11.1%, 20%, and 33.3%, respectively; the sensitivity of high differentiation was 0% versus 36.8% for poor differentiation. There was no correlation between plasma cfDNA concentration and patient characteristics. Conclusion We recommend using plasma cfDNA as a biomarker in stage IIIA or poorly differentiated tumors for gene diagnosis, especially in patients whose tissue samples cannot be obtained by surgery. Plasma samples can really reflect the patients’ EGFR mutation types and may contain comprehensive genotypic information that comes from different parts of the tumor than tissue specimens. The concentration of plasma cfDNA does not vary with patient characteristics.
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Affiliation(s)
- Kai Guo
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - ZhiPei Zhang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Lu Han
- Department of Ultrasound, Xijing Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jing Han
- Department of Ophthalmology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jian Wang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - YongAn Zhou
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - HongGang Liu
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - LiPing Tong
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - XiaoFei Li
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - XiaoLong Yan
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
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