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Junction Location Identifier (JuLI): Accurate Detection of DNA Fusions in Clinical Sequencing for Precision Oncology. J Mol Diagn 2019; 22:304-318. [PMID: 31881333 DOI: 10.1016/j.jmoldx.2019.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/04/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Accurate detection of genomic fusions by high-throughput sequencing in clinical samples with inadequate tumor purity and formalin-fixed, paraffin-embedded tissue is an essential task in precise oncology. We developed the fusion detection algorithm Junction Location Identifier (JuLI) for optimization of high-depth clinical sequencing. Novel filtering steps were implemented to minimize false positives in the clinical setting. The algorithm was comprehensively validated using high-depth sequencing data from cancer cell lines and clinical samples and genome sequencing data from NA12878. JuLI showed improved performance mainly in positive predictive value over state-of-the-art fusion callers in cases with high-depth clinical sequencing and rescued a driver fusion from false negative in plasma cell-free DNA using joint calling.
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Papadopoulou E, Tsoulos N, Tsantikidi K, Metaxa-Mariatou V, Stamou PE, Kladi-Skandali A, Kapeni E, Tsaousis G, Pentheroudakis G, Petrakis D, Lampropoulou DI, Aravantinos G, Varthalitis I, Kesisis G, Boukovinas I, Papakotoulas P, Katirtzoglou N, Athanasiadis E, Stavridi F, Christodoulou C, Koumarianou A, Eralp Y, Nasioulas G. Clinical feasibility of NGS liquid biopsy analysis in NSCLC patients. PLoS One 2019; 14:e0226853. [PMID: 31860648 PMCID: PMC6924668 DOI: 10.1371/journal.pone.0226853] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background Analysis of circulating tumor nucleic acids in plasma of Non-Small Cell Lung Cancer (NSCLC) patients is the most widespread and documented form of "liquid biopsy" and provides real-time information on the molecular profile of the tumor without an invasive tissue biopsy. Methods Liquid biopsy analysis was requested by the referral physician in 121 NSCLC patients at diagnosis and was performed using a sensitive Next Generation Sequencing assay. Additionally, a comparative analysis of NSCLC patients at relapse following EGFR Tyrosine Kinase Inhibitor (TKIs) treatment was performed in 50 patients by both the cobas and NGS platforms. Results At least one mutation was identified in almost 49% of the cases by the NGS approach in NSCLC patients analyzed at diagnosis. In 36 cases with paired tissue available a high concordance of 86.11% was observed for clinically relevant mutations, with a Positive Predictive Value (PPV) of 88.89%. Furthermore, a concordance rate of 82% between cobas and the NGS approach for the EGFR sensitizing mutations (in exons 18, 19, 21) was observed in patients with acquired resistance to EGFR TKIs, while this concordance was 94% for the p.T790M mutation, with NGS being able to detect this mutation in three 3 additional patients. Conclusions This study indicates the feasibility of circulating tumor nucleic acids (ctNA) analysis as a tumor biopsy surrogate in clinical practice for NSCLC personalized treatment decision making. The use of new sensitive NGS techniques can reliably detect tumor-derived mutations in liquid biopsy and provide clinically relevant information both before and after targeted treatment in patients with NSCLC. Thus, it could aid physicians in treatment decision making in clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - George Pentheroudakis
- Department of Medical Oncology, School of Medicine, Ioannina, Greece
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Dimitrios Petrakis
- Department of Medical Oncology, School of Medicine, Ioannina, Greece
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | | | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | - George Kesisis
- Oncology Department, Saint Luke Private Hospital, Thessaloniki, Greece
| | | | - Pavlos Papakotoulas
- First Department of Clinical Oncology, Theagenio Hospital, Thessaloniki, Greece
| | | | | | - Flora Stavridi
- Fourth Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | - Anna Koumarianou
- Hematology Oncology Unit, Fourth Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Yeşim Eralp
- Department of Medical Oncology, Istanbul University School of Medicine, İstanbul, Turkey
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de Melo-Silva AJ, Lucena JP, Hueneburg T. The evolution of molecular diagnosis using digital polymerase chain reaction to detect cancer via cell-free DNA and circulating tumor cells. Cell Biol Int 2019; 44:735-743. [PMID: 31829466 DOI: 10.1002/cbin.11286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
Abstract
Cancer is one of the most important causes of death worldwide. The onset of cancer may be initiated due to a variety of factors such as environment, genetics or even due to personal lifestyle choices. To counteract this tremendous increase, the demand for a new technology has risen. By this means, the use of digital polymerase chain reaction (dPCR) has been shown to be a promising methodology in the early detection of many types of cancers. Furthermore, several researchers confirmed that the use of tumor cell-free DNA (cfDNA) and circulating tumor cells (CTC) in peripheral blood is essential in revealing an early prognosis of such diseases. Besides this, it was established that dPCR might be used in a much more efficient, accurate, and reliable manner to amplify a variety of genetic material up to the identification of mutations in hematological diseases. Therefore, this article demonstrates the differences between conventional PCR and dPCR as a molecular technique to detect the early onset of cancer. Furthermore, CTC and cfDNA were officially approved by the Food and Drug Administration as new biological biomarkers in cancer development and monitoring.
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Affiliation(s)
- Alex José de Melo-Silva
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Jessica Paula Lucena
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Thomas Hueneburg
- University of Technology Sydney, Sydney, 2007, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne-Vic, 3010 Parkeville VIC, Australia
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Kondrashova O, Ho GY, Au-Yeung G, Leas L, Boughtwood T, Alsop K, Zapparoli G, Dobrovic A, Ko YA, Hsu AL, Love CJ, Lunke S, Wakefield MJ, McNally O, Quinn M, Ananda S, Neesham D, Hamilton A, Grossi M, Freimund A, Kanjanapan Y, Rischin D, Traficante N, Bowtell D, Scott CL, Christie M, Taylor GR, Mileshkin L, Waring PM. Clinical Utility of Real-Time Targeted Molecular Profiling in the Clinical Management of Ovarian Cancer: The ALLOCATE Study. JCO Precis Oncol 2019; 3:1-18. [DOI: 10.1200/po.19.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The ALLOCATE study was designed as a pilot to demonstrate the feasibility and clinical utility of real-time targeted molecular profiling of patients with recurrent or advanced ovarian cancer for identification of potential targeted therapies. PATIENTS AND METHODS A total of 113 patients with ovarian cancer of varying histologies were recruited from two tertiary hospitals, with 99 patient cases suitable for prospective analysis. Targeted molecular and methylation profiling of fresh biopsy and archived tumor samples were performed by screening for mutations or copy-number variations in 44 genes and for promoter methylation of BRCA1 and RAD51C. RESULTS Somatic genomic or methylation events were identified in 85% of all patient cases, with potentially actionable events with defined targeted therapies (including four resistance events) detected in 60% of all patient cases. On the basis of these findings, six patients received molecularly guided therapy, three patients had unsuspected germline cancer–associated BRCA1/ 2 mutations and were referred for genetic counseling, and two intermediate differentiated (grade 2) serous ovarian carcinomas were reclassified as low grade, leading to changes in clinical management. Additionally, secondary reversion mutations in BRCA1/ 2 were identified in fresh biopsy samples of two patients, consistent with clinical platinum/poly (ADP-ribose) polymerase inhibitor resistance. Timely reporting of results if molecular testing is done at disease recurrence, as well as early referral for patients with platinum-resistant cancers, were identified as factors that could improve the clinical utility of molecular profiling. CONCLUSION ALLOCATE molecular profiling identified known genomic and methylation alterations of the different ovarian cancer subtypes and was deemed feasible and useful in routine clinical practice. Better patient selection and access to a wider range of targeted therapies or clinical trials will further enhance the clinical utility of molecular profiling.
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Affiliation(s)
- Olga Kondrashova
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - George Au-Yeung
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Leakhena Leas
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Giada Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Yi-An Ko
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Arthur L. Hsu
- University of Melbourne, Melbourne, Victoria, Australia
| | - Clare J. Love
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew J. Wakefield
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Orla McNally
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Michael Quinn
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Sumitra Ananda
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Anne Hamilton
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marisa Grossi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison Freimund
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yada Kanjanapan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Danny Rischin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - David Bowtell
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L. Scott
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Michael Christie
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Graham R. Taylor
- University of Melbourne, Melbourne, Victoria, Australia
- King’s College London, London, United Kingdom
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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Negative regulators of cell death pathways in cancer: perspective on biomarkers and targeted therapies. Apoptosis 2019; 23:93-112. [PMID: 29322476 DOI: 10.1007/s10495-018-1440-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cancer is a primary cause of human fatality and conventional cancer therapies, e.g., chemotherapy, are often associated with adverse side-effects, tumor drug-resistance, and recurrence. Molecularly targeted therapy, composed of small-molecule inhibitors and immunotherapy (e.g., monoclonal antibody and cancer vaccines), is a less harmful alternative being more effective against cancer cells whilst preserving healthy tissues. Drug-resistance, however, caused by negative regulation of cell death signaling pathways, is still a challenge. Circumvention of negative regulators of cell death pathways or development of predictive and response biomarkers is, therefore, quintessential. This review critically discusses the current state of knowledge on targeting negative regulators of cell death signaling pathways including apoptosis, ferroptosis, necroptosis, autophagy, and anoikis and evaluates the recent advances in clinical and preclinical research on biomarkers of negative regulators. It aims to provide a comprehensive platform for designing efficacious polytherapies including novel agents for restoring cell death signaling pathways or targeting alternative resistance pathways to improve the chances for antitumor responses. Overall, it is concluded that nonapoptotic cell death pathways are a potential research arena for drug discovery, development of novel biomarkers and targeted therapies.
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57
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Chen Z, Zhang C, Zhang M, Li B, Niu Y, Chen L, Yang J, Lu S, Gao J, Shen L. Chromosomal instability of circulating tumor DNA reflect therapeutic responses in advanced gastric cancer. Cell Death Dis 2019; 10:697. [PMID: 31541076 PMCID: PMC6754425 DOI: 10.1038/s41419-019-1907-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
Abstract
Gastric cancer is characterized by chromosomal instability. In this study, we investigated chromosomal instability quantified by copy number instability (CNI) score of circulating tumor DNA (ctDNA) during the drug treatment in advanced gastric cancer (AGC). A total of 55 pretherapeutic plasmas from 55 AGC patients and 75 plasmas during drug treatment of 26 AGC patients were collected. Plasma ctDNA was extracted and assessed by whole-genome sequencing (WGS) for somatic copy number alteration (SCNA), and according to which we calculated the CNI scores. We next assessed the correlations between chromosomal instability and therapeutic response. The cutoff value of chromosomal instability was defined as the mean + SD of the CNI scores (56.60) in cfDNA of plasmas from 100 healthy people. For 55 enrolled cases, chromosomal instability was observed in 27 (49%) prior to drug treatment, whose response rate (59%, 16/27) was higher than in 28 patients with stable chromosomes (32%, 9/28, P = 0.043). We also observed that CNI scores fluctuated during treatment in 26 patients. Specifically, the CNI scores in 93% (14/15) of patients sensitive to drug treatment reduced to the level of chromosomal stability and the CNI scores in 52% (13/25) of patients resistant to treatment elevated again. For ctDNA with developed resistance, the SCNA patterns were identical to those before treatment, whereas the CNI scores were lower than the pretherapeutic scores. We found that chromosomal instability based on ctDNA could predict and monitor therapeutic response in gastric cancer, although validation in a larger cohort will be necessary.
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Affiliation(s)
- Zuhua Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Cheng Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Mengqi Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Beifang Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yunyun Niu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China
| | - Limeng Chen
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China
| | - Jing Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics Co. Ltd., Shanghai, China.
| | - Jing Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China.
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China.
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58
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Moosavi F, Giovannetti E, Saso L, Firuzi O. HGF/MET pathway aberrations as diagnostic, prognostic, and predictive biomarkers in human cancers. Crit Rev Clin Lab Sci 2019; 56:533-566. [PMID: 31512514 DOI: 10.1080/10408363.2019.1653821] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer is a major cause of death worldwide. MET tyrosine kinase receptor [MET, c-MET, hepatocyte growth factor (HGF) receptor] pathway activation is associated with the appearance of several hallmarks of cancer. The HGF/MET pathway has emerged as an important actionable target across many solid tumors; therefore, biomarker discovery becomes essential in order to guide clinical intervention and patient stratification with the aim of moving towards personalized medicine. The focus of this review is on how the aberrant activation of the HGF/MET pathway in tumor tissue or the circulation can provide diagnostic and prognostic biomarkers and predictive biomarkers of drug response. Many meta-analyses have shown that aberrant activation of the MET pathway in tumor tissue, including MET gene overexpression, gene amplification, exon 14 skipping and other activating mutations, is almost invariably associated with shorter survival and poor prognosis. Most meta-analyses have been performed in non-small cell lung cancer (NSCLC), breast, head and neck cancers as well as colorectal, gastric, pancreatic and other gastrointestinal cancers. Furthermore, several studies have shown the predictive value of MET biomarkers in the identification of patients who gain the most benefit from HGF/MET targeted therapies administered as single or combination therapies. The highest predictive values have been observed for response to foretinib and savolitinib in renal cancer, as well as tivantinib in NSCLC and colorectal cancer. However, some studies, especially those based on MET expression, have failed to show much value in these stratifications. This may be rooted in lack of standardization of methodologies, in particular in scoring systems applied in immunohistochemistry determinations or absence of oncogenic addiction of cancer cells to the MET pathway, despite detection of overexpression. Measurements of amplification and mutation aberrations are less likely to suffer from these pitfalls. Increased levels of MET soluble ectodomain (sMET) in circulation have also been associated with poor prognosis; however, the evidence is not as strong as it is with tissue-based biomarkers. As a diagnostic biomarker, sMET has shown its value in distinguishing cancer patients from healthy individuals in prostate and bladder cancers and in melanoma. On the other hand, increased circulating HGF has also been presented as a valuable prognostic and diagnostic biomarker in many cancers; however, there is controversy on the predictive value of HGF as a biomarker. Other biomarkers such as circulating tumor DNA (ctDNA) and tumor HGF levels have also been briefly covered. In conclusion, HGF/MET aberrations can provide valuable diagnostic, prognostic and predictive biomarkers and represent vital assets for personalized cancer therapy.
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Affiliation(s)
- Fatemeh Moosavi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc) , Amsterdam , The Netherlands.,Cancer Pharmacology Lab, AIRC Start Up Unit, Fondazione Pisana per la Scienza Onlus , Pisa , Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology, "Vittorio Erspamer," Sapienza University , Rome , Italy
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
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Lee EY, Kulkarni RP. Circulating biomarkers predictive of tumor response to cancer immunotherapy. Expert Rev Mol Diagn 2019; 19:895-904. [PMID: 31469965 DOI: 10.1080/14737159.2019.1659728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction: The advent of checkpoint blockade immunotherapy has revolutionized cancer treatment, but clinical response to immunotherapies is highly heterogeneous among individual patients and between cancer types. This represents a challenge to oncologists when choosing specific immunotherapies for personalized medicine. Thus, biomarkers that can predict tumor responsiveness to immunotherapies before and during treatment are invaluable. Areas covered: We review the latest advances in 'liquid biopsy' biomarkers for noninvasive prediction and in-treatment monitoring of tumor response to immunotherapy, focusing primarily on melanoma and non-small cell lung cancer. We concentrate on high-quality studies published within the last five years on checkpoint blockade immunotherapies, and highlight significant breakthroughs, identify key areas for improvement, and provide recommendations for how these diagnostic tools can be translated into clinical practice. Expert opinion: The first biomarkers proposed to predict tumor response to immunotherapy were based on PD1/PDL1 expression, but their predictive value is limited to specific cancers or patient populations. Recent advances in single-cell molecular profiling of circulating tumor cells and host cells using next-generation sequencing has dramatically expanded the pool of potentially useful predictive biomarkers. As immunotherapy moves toward personalized medicine, a composite panel of both genomic and proteomic biomarkers will have enormous utility in therapeutic decision-making.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, UCLA , Los Angeles , CA , USA.,Department of Dermatology, UCLA , Los Angeles , CA , USA.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine at UCLA , Los Angeles , CA , USA
| | - Rajan P Kulkarni
- Department of Dermatology, OHSU , Portland , OR , USA.,Cancer Early Detection and Advanced Research Center (CEDAR), Knight Cancer Institute (KCI), OHSU , Portland , OR , USA.,Division of Operative Care, Portland VA Medical Center (PVAMC) , Portland , OR , USA
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60
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Jeffery M, Hickey BE, Hider PN. Follow-up strategies for patients treated for non-metastatic colorectal cancer. Cochrane Database Syst Rev 2019; 9:CD002200. [PMID: 31483854 PMCID: PMC6726414 DOI: 10.1002/14651858.cd002200.pub4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND This is the fourth update of a Cochrane Review first published in 2002 and last updated in 2016.It is common clinical practice to follow patients with colorectal cancer for several years following their curative surgery or adjuvant therapy, or both. Despite this widespread practice, there is considerable controversy about how often patients should be seen, what tests should be performed, and whether these varying strategies have any significant impact on patient outcomes. OBJECTIVES To assess the effect of follow-up programmes (follow-up versus no follow-up, follow-up strategies of varying intensity, and follow-up in different healthcare settings) on overall survival for patients with colorectal cancer treated with curative intent. Secondary objectives are to assess relapse-free survival, salvage surgery, interval recurrences, quality of life, and the harms and costs of surveillance and investigations. SEARCH METHODS For this update, on 5 April 2109 we searched CENTRAL, MEDLINE, Embase, CINAHL, and Science Citation Index. We also searched reference lists of articles, and handsearched the Proceedings of the American Society for Radiation Oncology. In addition, we searched the following trials registries: ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform. We contacted study authors. We applied no language or publication restrictions to the search strategies. SELECTION CRITERIA We included only randomised controlled trials comparing different follow-up strategies for participants with non-metastatic colorectal cancer treated with curative intent. DATA COLLECTION AND ANALYSIS We used standard methodological procedures expected by Cochrane. Two review authors independently determined study eligibility, performed data extraction, and assessed risk of bias and methodological quality. We used GRADE to assess evidence quality. MAIN RESULTS We identified 19 studies, which enrolled 13,216 participants (we included four new studies in this second update). Sixteen out of the 19 studies were eligible for quantitative synthesis. Although the studies varied in setting (general practitioner (GP)-led, nurse-led, or surgeon-led) and 'intensity' of follow-up, there was very little inconsistency in the results.Overall survival: we found intensive follow-up made little or no difference (hazard ratio (HR) 0.91, 95% confidence interval (CI) 0.80 to 1.04: I² = 18%; high-quality evidence). There were 1453 deaths among 12,528 participants in 15 studies. In absolute terms, the average effect of intensive follow-up on overall survival was 24 fewer deaths per 1000 patients, but the true effect could lie between 60 fewer to 9 more per 1000 patients.Colorectal cancer-specific survival: we found intensive follow-up probably made little or no difference (HR 0.93, 95% CI 0.81 to 1.07: I² = 0%; moderate-quality evidence). There were 925 colorectal cancer deaths among 11,771 participants enrolled in 11 studies. In absolute terms, the average effect of intensive follow-up on colorectal cancer-specific survival was 15 fewer colorectal cancer-specific survival deaths per 1000 patients, but the true effect could lie between 47 fewer to 12 more per 1000 patients.Relapse-free survival: we found intensive follow-up made little or no difference (HR 1.05, 95% CI 0.92 to 1.21; I² = 41%; high-quality evidence). There were 2254 relapses among 8047 participants enrolled in 16 studies. The average effect of intensive follow-up on relapse-free survival was 17 more relapses per 1000 patients, but the true effect could lie between 30 fewer and 66 more per 1000 patients.Salvage surgery with curative intent: this was more frequent with intensive follow-up (risk ratio (RR) 1.98, 95% CI 1.53 to 2.56; I² = 31%; high-quality evidence). There were 457 episodes of salvage surgery in 5157 participants enrolled in 13 studies. In absolute terms, the effect of intensive follow-up on salvage surgery was 60 more episodes of salvage surgery per 1000 patients, but the true effect could lie between 33 to 96 more episodes per 1000 patients.Interval (symptomatic) recurrences: these were less frequent with intensive follow-up (RR 0.59, 95% CI 0.41 to 0.86; I² = 66%; moderate-quality evidence). There were 376 interval recurrences reported in 3933 participants enrolled in seven studies. Intensive follow-up was associated with fewer interval recurrences (52 fewer per 1000 patients); the true effect is between 18 and 75 fewer per 1000 patients.Intensive follow-up probably makes little or no difference to quality of life, anxiety, or depression (reported in 7 studies; moderate-quality evidence). The data were not available in a form that allowed analysis.Intensive follow-up may increase the complications (perforation or haemorrhage) from colonoscopies (OR 7.30, 95% CI 0.75 to 70.69; 1 study, 326 participants; very low-quality evidence). Two studies reported seven colonoscopic complications in 2292 colonoscopies, three perforations and four gastrointestinal haemorrhages requiring transfusion. We could not combine the data, as they were not reported by study arm in one study.The limited data on costs suggests that the cost of more intensive follow-up may be increased in comparison with less intense follow-up (low-quality evidence). The data were not available in a form that allowed analysis. AUTHORS' CONCLUSIONS The results of our review suggest that there is no overall survival benefit for intensifying the follow-up of patients after curative surgery for colorectal cancer. Although more participants were treated with salvage surgery with curative intent in the intensive follow-up groups, this was not associated with improved survival. Harms related to intensive follow-up and salvage therapy were not well reported.
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Affiliation(s)
- Mark Jeffery
- Christchurch HospitalCanterbury Regional Cancer and Haematology ServicePrivate Bag 4710ChristchurchNew Zealand8140
| | - Brigid E Hickey
- Princess Alexandra HospitalRadiation Oncology Mater Service31 Raymond TerraceBrisbaneQueenslandAustralia4101
- The University of QueenslandSchool of MedicineBrisbaneAustralia
| | - Phillip N Hider
- University of Otago, ChristchurchDepartment of Population HealthPO Box 4345ChristchurchNew Zealand8140
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Hojbjerg JA, Madsen AT, Schmidt HH, Sorensen SF, Stougaard M, Meldgaard P, Sorensen BS. Intra-individual variation of circulating tumour DNA in lung cancer patients. Mol Oncol 2019; 13:2098-2106. [PMID: 31306545 PMCID: PMC6763781 DOI: 10.1002/1878-0261.12546] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Circulating tumour DNA (ctDNA) has been increasingly incorporated into the treatment of cancer patients. ctDNA is generally accepted as a powerful diagnostic tool, whereas the utility of ctDNA to monitor disease activity needs to be fully validated. Central to this challenge is the question of whether changes in longitudinal ctDNA measurements reflect disease activity or merely biological variation. Thus, the aim of this study was to explore the intra‐individual biological variation of ctDNA in lung cancer patients. We identified tumour‐specific mutations using next‐generation sequencing. Day‐to‐day and hour‐to‐hour variations in plasma concentrations of the mutant allele and wild‐type cell‐free DNA (cfDNA) were determined using digital PCR. The levels of the mutant alleles varied by as much as 53% from day to day and 27% from hour to hour. cfDNA varied up to 19% from day to day and up to 56% from hour to hour, as determined using digital PCR. Variations were independent of the concentration. Both mutant allele concentrations and wild‐type cfDNA concentrations showed considerable intra‐individual variation in lung cancer patients with nonprogressive disease. This pronounced biological variation of the circulating DNA should be investigated further to determine whether ctDNA can be used for monitoring cancer activity.
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Affiliation(s)
- Johanne A Hojbjerg
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | - Anne T Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | - Steffen F Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
| | | | | | - Boe S Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Denmark
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Luchini C, Veronese N, Nottegar A, Cappelletti V, Daidone MG, Smith L, Parris C, Brosens LAA, Caruso MG, Cheng L, Wolfgang CL, Wood LD, Milella M, Salvia R, Scarpa A. Liquid Biopsy as Surrogate for Tissue for Molecular Profiling in Pancreatic Cancer: A Meta-Analysis Towards Precision Medicine. Cancers (Basel) 2019; 11:cancers11081152. [PMID: 31405192 PMCID: PMC6721631 DOI: 10.3390/cancers11081152] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy (LB) is a non-invasive approach representing a promising tool for new precision medicine strategies for cancer treatment. However, a comprehensive analysis of its reliability for pancreatic cancer (PC) is lacking. To this aim, we performed the first meta-analysis on this topic. We calculated the pooled sensitivity, specificity, positive (LR+) and negative (LR−) likelihood ratio, and diagnostic odds ratio (DOR). A summary receiver operating characteristic curve (SROC) and area under curve (AUC) were used to evaluate the overall accuracy. We finally assessed the concordance rate of all mutations detected by multi-genes panels. Fourteen eligible studies involving 369 patients were included. The overall pooled sensitivity and specificity were 0.70 and 0.86, respectively. The LR+ was 3.85, the LR- was 0.34 and DOR was 15.84. The SROC curve with an AUC of 0.88 indicated a relatively high accuracy of LB for molecular characterization of PC. The concordance rate of all mutations detected by multi-genes panels was 31.9%. LB can serve as surrogate for tissue in the molecular profiling of PC, because of its relatively high sensitivity, specificity and accuracy. It represents a unique opportunity to be further explored towards its introduction in clinical practice and for developing new precision medicine approaches against PC.
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Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
| | - Nicola Veronese
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Castellana Grotte, 70013 Bari, Italy
| | - Alessia Nottegar
- Department of Surgery, Section of Pathology, San Bortolo Hospital, 36100 Vicenza, Italy
| | - Vera Cappelletti
- Applied Research and Technological Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133 Milano, Italy
| | - Maria G Daidone
- Applied Research and Technological Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133 Milano, Italy
| | - Lee Smith
- Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Christopher Parris
- Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Lodewijk A A Brosens
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6526GA Nijmegen, The Netherlands
| | - Maria G Caruso
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Castellana Grotte, 70013 Bari, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christopher L Wolfgang
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
- Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Roberto Salvia
- Department of General and Visceral Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy.
- ARC-Net Research Center, University of Verona, 37134 Verona, Italy.
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Chiu KP, Yu AL. Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions. PeerJ 2019; 7:e7426. [PMID: 31404440 PMCID: PMC6688590 DOI: 10.7717/peerj.7426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/07/2019] [Indexed: 12/29/2022] Open
Abstract
It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. Multiple studies using microbial cfDNA sequencing to identify microbes for septic patients have shown strong agreement with cell culture. Similar approaches have also been applied to reveal previously unidentified microorganisms or to demonstrate the feasibility of comprehensive assessment of bloodborne microorganisms for healthy and/or diseased individuals. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in various environments. This article reviews this line of research and discuss the methodological approaches that have been developed, or are likely to be developed in the future, which may have strong potential to facilitate cfDNA- and cfRNA-based studies of cancer and acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases.
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Affiliation(s)
- Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Departent of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Alice L Yu
- Department of Pediatrics, University of California, San Diego, San Diego, United States of America.,Institute of Stem Cell and Translational Cancer Research, Chang Gung University, Taipei, Taiwan
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Oellerich M, Christenson RH, Beck J, Walson PD. Plasma EGFR mutation testing in non-small cell lung cancer: A value proposition. Clin Chim Acta 2019; 495:481-486. [DOI: 10.1016/j.cca.2019.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022]
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Circulating Cell-Free DNA-Diagnostic and Prognostic Applications in Personalized Cancer Therapy. Ther Drug Monit 2019; 41:115-120. [PMID: 30883505 DOI: 10.1097/ftd.0000000000000566] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Genomic analyses in oncologic care allow for the development of more precise clinical laboratory tests that will be critical for personalized pharmacotherapy. Traditional biopsy-based approaches are limited by the availability of sequential tissue specimens to detect resistance. Blood-based genomic profiling ("liquid biopsy") is useful for longitudinal monitoring of tumor genomes and can complement biopsies. Tumor-associated mutations can be identified in cell-free tumor DNA (ctDNA) from patient blood samples and used for monitoring disease activity. The US Food and Drug Administration approved a liquid biopsy test for EGFR-activating mutations in patients with non-small-cell lung cancer as a companion diagnostic for therapy selection. ctDNA also allows for the identification of mutations selected by treatment such as EGFR T790M in non-small-cell lung cancer. ctDNA can also detect mutations such as KRAS G12V in colorectal cancer and BRAF V600E/V600K in melanoma. Chromosomal aberration pattern analysis by low-coverage whole genome sequencing is a new, broader approach. Genomic imbalances detected in cell-free DNA (cfDNA) can be used to compute a copy number instability (CNI) score. In clinical studies, it was demonstrated that the change in CNI score can serve as an early predictor of therapeutic response to chemotherapy/immunotherapy of many cancer types. In multivariable models, it could be shown that the CNI score was superior to clinical parameters for prediction of overall survival in patients with head and neck cancer. There is emerging evidence for the clinical validity of ctDNA testing regarding identification of candidates for targeted therapies, prediction of therapeutic response, early detection of recurrence, resistance mutation detection, measuring genetic heterogeneity, tumor burden monitoring, and risk stratification. Improvement of sensitivity to detect tumors at very early stages is difficult due to insufficient mutant DNA fraction of ≤0.01%. Further developments will include validation in prospective multicenter interventional outcome studies and the development of digital platforms to integrate diagnostic data.
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Henare KL, Parker KE, Wihongi H, Blenkiron C, Jansen R, Reid P, Findlay MP, Lawrence B, Hudson M, Print CG. Mapping a route to Indigenous engagement in cancer genomic research. Lancet Oncol 2019; 20:e327-e335. [DOI: 10.1016/s1470-2045(19)30307-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/23/2022]
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Kowalczyk A, Krajczewski J, Kowalik A, Weyher JL, Dzięcielewski I, Chłopek M, Góźdź S, Nowicka AM, Kudelski A. New strategy for the gene mutation identification using surface enhanced Raman spectroscopy (SERS). Biosens Bioelectron 2019; 132:326-332. [DOI: 10.1016/j.bios.2019.03.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/05/2023]
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Abstract
Genetic material derived from tumours is constantly shed into the circulation of cancer patients both in the form of circulating free nucleic acids and within circulating cells or extracellular vesicles. Monitoring cancer-specific genomic alterations, particularly mutant allele frequencies, in circulating nucleic acids allows for a non-invasive liquid biopsy for detecting residual disease and response to therapy. The advent of molecular targeted treatments and immunotherapies with increasing effectiveness requires corresponding effective molecular biology methods for the detection of biomarkers such as circulating nucleic acid to monitor and ultimately personalise therapy. The use of polymerase chain reaction (PCR)-based methods, such as droplet digital PCR, allows for a very sensitive analysis of circulating tumour DNA, but typically only a limited number of gene mutations can be detected in parallel. In contrast, next-generation sequencing allows for parallel analysis of multiple mutations in many genes. The development of targeted next-generation sequencing cancer gene panels optimised for the detection of circulating free DNA now provides both the flexibility of multiple mutation analysis coupled with a sensitivity that approaches or even matches droplet digital PCR. In this review, we discuss the advantages and disadvantages of these current molecular technologies in conjunction with how this field is evolving in the context of melanoma diagnosis, prognosis, and monitoring of response to therapy.
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Kacerovsky M, Vlkova B, Musilova I, Andrys C, Pliskova L, Zemlickova H, Stranik J, Halada P, Jacobsson B, Celec P. Amniotic fluid cell-free DNA in preterm prelabor rupture of membranes. Prenat Diagn 2018; 38:1086-1095. [PMID: 30276834 DOI: 10.1002/pd.5366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION We evaluated the levels of cell-free nuclear DNA (nDNA) and cell-free mitochondrial DNA (mtDNA) in the amniotic fluid supernatant from pregnancies complicated by preterm prelabor rupture of membranes (PPROM) based on evidence of microbial invasion of the amniotic cavity (MIAC) and/or intra-amniotic inflammation (IAI). MATERIAL AND METHODS A total of 155 women with PPROM were included in this study. Amniotic fluid samples were obtained by transabdominal amniocentesis. The levels of cell-free nDNA and mtDNA in the amniotic fluid supernatant were assessed and quantified by real-time polymerase chain reaction. RESULTS The levels of cell-free nDNA and mtDNA were higher in women with MIAC and IAI than in women without these conditions (nDNA: with MIAC: median 3.9 × 104 genome equivalent [GE]/mL vs without MIAC: median 1.2 × 104 GE/mL, with IAI: median: 5.3 × 104 GE/mL vs without IAI: median 1.2 × 104 GE/mL; mtDNA: with MIAC: median 9.2 × 105 GE/mL vs without MIAC: median 2.5 × 105 GE/mL, with IAI: median 1.1 × 106 GE/mL vs without IAI: median 2.5 × 105 ; all P values ≤ 0.01). Women with the microbial-associated IAI showed the highest levels of cell-free nDNA and mtDNA. CONCLUSIONS Cell-free nDNA and mtDNA are constituents of the amniotic fluid supernatant from PPROM pregnancies. Both cell-free nDNA and mtDNA are involved in the intra-amniotic inflammatory response in women with PPROM.
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Affiliation(s)
- Marian Kacerovsky
- Department of Obstetrics and Gynecology, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Barbora Vlkova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Department of Clinical Immunology and Allergy, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Lenka Pliskova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Helena Zemlickova
- Institute of Clinical Microbiology, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jaroslav Stranik
- Department of Obstetrics and Gynecology, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Petr Halada
- Department of Obstetrics and Gynecology, Charles University, Faculty of Medicine Hradec Kralove, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.,Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
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Abstract
Early detection of ovarian cancer could reduce mortality by 10% to 30%. Effective screening requires high sensitivity (>75%) and extremely high specificity (99.7%). Clinical trials suggest the best specificity is achieved with 2-stage strategies in which increasing serum CA125 level triggers transvaginal sonography to detect a malignant pelvic mass, although evidence for such approaches improving overall survival has been limited. Screening may be improved by combining CA125 with novel biomarkers, such as autoantibodies, circulating tumor DNA, or microRNAs. In order to detect premetastatic ovarian cancers originating in the distal fallopian tube, more sensitive approaches to diagnostic imaging are required.
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Affiliation(s)
- Kevin M Elias
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
| | - Jing Guo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University, 301 Yanchang Road, Jingan, Shanghai 200072, China
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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Anderson EM, Maldarelli F. Quantification of HIV DNA Using Droplet Digital PCR Techniques. ACTA ACUST UNITED AC 2018; 51:e62. [PMID: 30253074 DOI: 10.1002/cpmc.62] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HIV persists, despite effective antiretroviral therapy, in long-lived cells, posing a major barrier toward a cure. A key step in the HIV replication cycle and a hallmark of the Retroviridae family is the integration of the viral DNA into the host genome. Once integrated, HIV expression is regulated by host machinery and the provirus persists until the cell dies. A reservoir of cells harboring replication-competent proviruses can survive for years, and mechanisms that maintain that reservoir are under investigation. The majority of integrated proviruses, however, are defective or have large deletions, and the composition of the proviral landscape during therapy remains unknown. Methods to quantify HIV proviruses are useful in investigating HIV persistence. Presented in this unit is a method for total HIV DNA quantification of various HIV genome targets that utilizes the next-generation PCR platform, digital PCR. The abundance of various HIV gene targets reflects the overall proviral composition. In this protocol, total genomic DNA is isolated from patient-derived cells and then used as a template for droplet digital PCR, in which the PCR reaction is partitioned into approximately 20,000 individual droplets, PCR amplified to an end point, and subjected to absolute quantification by counting the number of positive and negative droplets. Copy number is directly calculated using straightforward Poisson correction. Additionally, this methodological approach can be used to obtain absolute quantification of other DNA targets. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
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72
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Denis JA, Guillerm E, Coulet F, Larsen AK, Lacorte JM. The Role of BEAMing and Digital PCR for Multiplexed Analysis in Molecular Oncology in the Era of Next-Generation Sequencing. Mol Diagn Ther 2018; 21:587-600. [PMID: 28667577 DOI: 10.1007/s40291-017-0287-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BEAMing polymerase chain reaction (PCR) and digital PCR (dPCR) are used for robust and accurate quantification of nucleic acids. These methods are particularly well suited for the identification of very small fractions (<1%) of variant copies such as the presence of mutant genes in a predominantly wild-type background. BEAMing and dPCR are increasingly used in diverse fields including bacteriology, virology, non-invasive prenatal testing, and oncology, in particular for the molecular analysis of liquid biopsies. In this review, we present the principles of BEAMing and dPCR as well as the trends of future technical development, focusing on the possibility of developing multiplexed mutation analysis. Finally, we will discuss why such techniques will remain useful despite the ever-decreasing costs and increased automatization of next-generation sequencing (NGS), using molecular characterization of cancer cells as an example.
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Affiliation(s)
- Jérôme Alexandre Denis
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France. .,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France. .,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France.
| | - Erell Guillerm
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Florence Coulet
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Annette K Larsen
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France
| | - Jean-Marc Lacorte
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMR_S 1166, Research Institute of Cardiovascular Disease, Metabolism and Nutrition, 75013, Paris, France.,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France
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Abdullaev S, Minkabirova G, Karmanova E, Bruskov V, Gaziev A. Metformin prolongs survival rate in mice and causes increased excretion of cell-free DNA in the urine of X-irradiated rats. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 831:13-18. [PMID: 29875072 DOI: 10.1016/j.mrgentox.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/25/2018] [Accepted: 05/04/2018] [Indexed: 12/25/2022]
Abstract
An antidiabetic drug metformin has anticarcinogenic and geroprotective effects and has been used in combination with radiation cancer therapy. The present work is devoted to the study of the effect of metformin on survival in mice, the frequency of micronuclei in mouse bone marrow cells and excretion of cell-free nuclear and mitochondrial DNA in the urine of X-ray-exposed rats. The survival rate and the frequency of micronuclei in mice and excretion of DNA into rat urine were determined after administration of the drug before and after irradiation of animals. The DNA content was measured by qRT-PCR. Metformin shows a radioprotective effect only when administered to mice after the radiation exposure. On the 11th day after irradiation, we observed 100% mortality in the control group; 78% of mice remained alive if metformin was given. Twenty percent of the mice in this group survived for 30 days after irradiation. Metformin has the same effect on the frequency of micronuclei; its reduction is observed, when the drug is administered to the mice after irradiation. Metformin promotes the excretion of nuclear and mitochondrial DNA with the urine of irradiated rats. The results show that metformin acts as a radiomitigation effector. Metformin promotes the active excretion of DNA of dying cells from the tissues of irradiated animals.
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Affiliation(s)
- Serazhutdin Abdullaev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation.
| | - Gulchachak Minkabirova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation.
| | - Ekaterina Karmanova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation; Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russian Federation.
| | - Vadim Bruskov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation; Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russian Federation.
| | - Azhub Gaziev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation.
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74
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Ho J, Li X, Zhang L, Liang Y, Hu W, Yau JCW, Chan H, Gin T, Chan MTV, Tse G, Wu WKK. Translational genomics in pancreatic ductal adenocarcinoma: A review with re-analysis of TCGA dataset. Semin Cancer Biol 2018; 55:70-77. [PMID: 29705685 DOI: 10.1016/j.semcancer.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022]
Abstract
Malignancy of the pancreas is a leading cause of cancer-related mortality, with the highest case-fatality of all cancers. Nevertheless, the lack of sensitive biomarkers and presence of biological heterogeneity precludes its early detection and effective treatment. The recent introduction of next-generation sequencing allows characterization of multiple driver mutations at genome- and exome-wide levels. Sequencing of DNA and RNA from circulating tumour cells has also opened an exciting era of non-invasive procedures for tumour detection and prognostication. This massively-parallel sequencing technology has uncovered the previously obscure molecular mechanisms, providing clues for better stratification of patients and identification of druggable targets for the disease. Identification of active oncogenic pathways and gene-gene interactions may reveal oncogene addiction and synthetic lethality. Relevant findings can be extrapolated to develop targeted and personalized therapeutic interventions. In addition to known mutational events, the role of chromosomal rearrangements in pancreatic neoplasms is gradually uncovered. Coupled with bioinformatics pipelines and epidemiological analyses, a better framework for risk stratification and prognostication of pancreatic cancer will be possible in the near future. In this review, we discuss how translational genomic studies facilitate our understanding of pathobiology, and development of novel diagnostics and therapeutics for pancreatic ductal adenocarcinoma with emphases on whole genome sequencing, whole exome sequencing, and liquid biopsies. We have also re-analyzed The Cancer Genome Atlas (TCGA) dataset to look for genetic features associated with altered survival in patients with pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jeffery Ho
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Xianchun Li
- State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 00060, China
| | - Lin Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Yonghao Liang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Hu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Johnny C W Yau
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hung Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Tony Gin
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - Gary Tse
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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75
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Wartman LD. The future of cancer treatment using precision oncogenomics. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002824. [PMID: 29610395 PMCID: PMC5880270 DOI: 10.1101/mcs.a002824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Clinicians should soon have the opportunity to use precision oncogenomics to tailor the optimal cancer treatment to a specific patient. Precision oncogenomics will incorporate different sequencing platforms depending on the goal of the sequencing result. For example, the sequencing strategy used in immuno-oncology for the design of a tumor-specific vaccine may be different than that used by oncologists following a patient for clearance of mutations from circulating tumor DNA in the peripheral blood. I will provide a broad overview of several of the ways that precision oncogenomics is likely to influence the field of oncology over the next several years building off the experience at the Genomics Tumor Board at Washington University in St. Louis and a case of small-cell neuroendocrine carcinoma of the endometrium as examples.
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Affiliation(s)
- Lukas D Wartman
- Washington University School of Medicine, St. Louis, Missouri 63110, USA
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76
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Feng WN, Gu WQ, Zhao N, Pan YM, Luo W, Zhang H, Liang JM, Yang J, Deng YM. Comparison of the SuperARMS and Droplet Digital PCR for Detecting EGFR Mutation in ctDNA From NSCLC Patients. Transl Oncol 2018. [PMID: 29525631 PMCID: PMC5884193 DOI: 10.1016/j.tranon.2018.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND: Liquid biopsy is emerging as an important approach for tumor genotyping in non-small cell lung cancer, ddPCR and SuperARMS are both methods with high sensitivity and specificity for detecting EGFR mutation in plasma. We aimed to compare ddPCR and SuperARMS to detect plasma EGFR status in a cohort of advanced NSCLC patients. METHOD: A total of 79 tumor tissues and paired plasma samples were collected. The EGFR mutation status in tissue was tested by ADx-ARMS, matched plasma was detected by ddPCR and SuperARMS, respectively. RESULTS: The EGFR mutation rates were identified as 64.6% (tissue, ARMS), 55.7% (plasma, ddPCR), and 49.4% (plasma, Super ARMS), respectively. The sensitivity of ddPCR was similar with Super-ARMS in plasma EGFR detection (80.4% vs 76.5%), as well as the specificity (89.3% vs 100%). And the McNemar’s test showed there was no significant difference (P = .125). The concordance rate between SuperARMS and ddPCR was 91.1%. A significant interaction was observed between cfDNA EGFR mutation status and EGFR-TKIs treatment tested by both methods. CONCLUSION: Super-ARMS and ddPCR share the similar accuracy for EGFR mutation detection in plasma biopsy; both methods predicted well the efficacy of EGFR-TKIs by detecting plasma EGFR status.
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Affiliation(s)
- Wei-Neng Feng
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, Guangdong, PR China
| | - Wei-Quan Gu
- Department of Thoracic Surgery, The First People's Hospital of Foshan, Foshan, PR China
| | - Ning Zhao
- Department of Thoracic Surgery, The First People's Hospital of Foshan, Foshan, PR China
| | - Ying-Ming Pan
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, PR China
| | - Wei Luo
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, PR China
| | - Hua Zhang
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, Guangdong, PR China
| | - Jian-Miao Liang
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, Guangdong, PR China
| | - Jie Yang
- Department of Thoracic Surgery, The First People's Hospital of Foshan, Foshan, PR China
| | - Yan-Ming Deng
- Department of Head and Neck/Thoracic Medical Oncology, The First People's Hospital of Foshan, Foshan, Guangdong, PR China.
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77
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Cardona AF, Zatarain-Barrón ZL, Rojas L, Arrieta O. The reality of complexity: concomitant genomic alterations in patients with EGFR mutations. J Thorac Dis 2018; 10:597-599. [PMID: 29608188 DOI: 10.21037/jtd.2017.12.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andrés F Cardona
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia.,Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Clinical Research and Biology Systems Department, Universidad el Bosque, Bogotá, Colombia
| | - Zyanya Lucia Zatarain-Barrón
- Thoracic Oncology Unit and Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), México City, Mexico
| | - Leonardo Rojas
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia.,Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Oncology Department, Sanitas Foundation, Clinica Colsanitas, Bogotá, Colombia
| | - Oscar Arrieta
- Thoracic Oncology Unit and Laboratory of Personalized Medicine, Instituto Nacional de Cancerología (INCan), México City, Mexico
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78
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Nörthen A, Asendorf T, Walson PD, Oellerich M. Diagnostic value of alpha-1-fetoprotein (AFP) as a biomarker for hepatocellular carcinoma recurrence after liver transplantation. Clin Biochem 2018; 52:20-25. [DOI: 10.1016/j.clinbiochem.2017.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/18/2017] [Accepted: 10/15/2017] [Indexed: 12/19/2022]
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79
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Morris S, Vachani A, Pass HI, Rom WN, Ryden K, Weiss GJ, Hogarth DK, Runger G, Richards D, Shelton T, Mallery DW. Whole blood FPR1 mRNA expression predicts both non-small cell and small cell lung cancer. Int J Cancer 2018; 142:2355-2362. [PMID: 29313979 PMCID: PMC5901395 DOI: 10.1002/ijc.31245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/13/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
While long‐term survival rates for early‐stage lung cancer are high, most cases are diagnosed in later stages that can negatively impact survival rates. We aim to design a simple, single biomarker blood test for early‐stage lung cancer that is robust to preclinical variables and can be readily implemented in the clinic. Whole blood was collected in PAXgene tubes from a training set of 29 patients, and a validation set of 260 patients, of which samples from 58 patients were prospectively collected in a clinical trial specifically for our study. After RNA was extracted, the expressions of FPR1 and a reference gene were quantified by an automated one‐step Taqman RT‐PCR assay. Elevated levels of FPR1 mRNA in whole blood predicted lung cancer status with a sensitivity of 55% and a specificity of 87% on all validation specimens. The prospectively collected specimens had a significantly higher 68% sensitivity and 89% specificity. Results from patients with benign nodules were similar to healthy volunteers. No meaningful correlation was present between our test results and any clinical characteristic other than lung cancer diagnosis. FPR1 mRNA levels in whole blood can predict the presence of lung cancer. Using this as a reflex test for positive lung cancer screening computed tomography scans has the potential to increase the positive predictive value. This marker can be easily measured in an automated process utilizing off‐the‐shelf equipment and reagents. Further work is justified to explain the source of this biomarker. What's new? There have been several lung cancer screening trials evaluating the potential benefit of imaging for improving survival outcomes in lung cancer patients. While low‐dose computed tomography (CT) screening reduces mortality, it yields a 96.4% false‐positive rate. A potential strategy to improve screening may be the identification of additional tools that improve identification of false positives. Using prospectively collected whole blood samples, here the authors show that elevated FPR1 mRNA expression has a 68% sensitivity and 89% specificity. This single biomarker blood test, which can be readily implemented in the clinic, may increase the positive predictive value of detecting lung cancer.
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Affiliation(s)
| | - Anil Vachani
- Penn Lung CenterUniversity of PennsylvaniaPhiladelphiaPA
| | - Harvey I. Pass
- Thoracic OncologyNew York University Langone Medical CenterNew YorkNY
| | - William N. Rom
- Thoracic OncologyNew York University Langone Medical CenterNew YorkNY
| | | | - Glen J. Weiss
- Department of Internal MedicineUniversity of Arizona College of Medicine‐PhoenixPhoenixAZ
| | - D. K. Hogarth
- Bronchoscopy and Minimally Invasive DiagnosticsUniversity of Chicago MedicineChicagoIL
| | - George Runger
- School of Biomedical DiagnosticsArizona State UniversityTempeAZ
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80
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Lee H, Choi M, Lim J, Jo M, Han JY, Kim TM, Cho Y. Magnetic Nanowire Networks for Dual-Isolation and Detection of Tumor-Associated Circulating Biomarkers. Theranostics 2018; 8:505-517. [PMID: 29290823 PMCID: PMC5743563 DOI: 10.7150/thno.21967] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/21/2017] [Indexed: 11/05/2022] Open
Abstract
Purpose: Recent developments in genomic and molecular methods have revolutionized the range of utilities of tumor-associated circulating biomarkers in both basic and clinical research. Herein, we present a novel approach for ultrasensitive extraction of cfDNA and CTCs, at high yield and purity, via the formation of magnetic nanowire networks. Materials and Methods: We fabricated and characterized biotinylated cationic polyethylenimine and biotinylated antibody cocktail-conjugated magnetic polypyrrole NWs (PEI/mPpy NW and Ab cocktail/mPpy NW, respectively). We applied these NWs to the extraction of cfDNA and CTC from the blood of 14 patients with lung cancer. We demonstrated reliable detection of EGFR mutations based on digital droplet PCR analysis of cfDNA and CTC DNA from patients with lung cancer. Results: The NW networks confined with a high density of magnetic nanoparticles exhibited superior saturation magnetization, which enabled rapid and high-yield capture whilst avoiding or minimizing damage and loss. The NW networks enabled the co-isolation of CTCs and cfDNA of high quality and sufficient quantities, thus allowing the amplification of rare and low-prevalence cancer-related mutations. Conclusion: The simple, versatile, and highly efficient nanowire network tool allows sensitive and robust assessment of clinical samples.
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81
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Peng L, Cantor DI, Huang C, Wang K, Baker MS, Nice EC. Tissue and plasma proteomics for early stage cancer detection. Mol Omics 2018; 14:405-423. [PMID: 30251724 DOI: 10.1039/c8mo00126j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pursuit of novel and effective biomarkers is essential in the struggle against cancer, which is a leading cause of mortality worldwide. Here we discuss the relative advantages and disadvantages of the most frequently used proteomics techniques, concentrating on the latest advances and application of tissue and plasma proteomics for novel cancer biomarker discovery.
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Affiliation(s)
- Liyuan Peng
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - David I. Cantor
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Macquarie University
- New South Wales
- Australia
| | - Canhua Huang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Kui Wang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University
- Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
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82
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Riethdorf S, Soave A, Rink M. The current status and clinical value of circulating tumor cells and circulating cell-free tumor DNA in bladder cancer. Transl Androl Urol 2017; 6:1090-1110. [PMID: 29354496 PMCID: PMC5760371 DOI: 10.21037/tau.2017.09.16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Urothelial carcinoma of the bladder (UCB) is a complex disease, which is associated with highly aggressive tumor biologic behavior, especially in patients with muscle-invasive and advanced tumors. Despite multimodal therapy options including surgery, radiotherapy and chemotherapy, UCB patients frequently suffer from poor clinical outcome. Indeed, the potential of diverse opportunities for modern targeted therapies is not sufficiently elucidated in UCB yet. To improve the suboptimal treatment situation in UCB, biomarkers are urgently needed that help detecting minimal residual disease (MRD), predicting therapy response and subsequently prognosis as well as enabling patient stratification for further therapies and therapy monitoring, respectively. To date, decision making regarding treatment planning is mainly based on histopathologic evaluation of biopsies predominantly derived from the primary tumors and on clinical staging. However, both methods are imperfect for sufficient outcome prediction. During disease progression, individual disseminated tumor cells and consecutively metastases can acquire characteristics that do not match those of the corresponding primary tumors, and often are only hardly assessable for further evaluation. Therefore, during recent years, strong efforts were directed to establish non-invasive biomarkers from liquid biopsies. Urine cytology and serum tumor markers have been established for diagnostic purposes, but are still insufficient as universal biomarkers for decision-making and treatment of UCB patients. To date, the clinical relevance of various newly established blood-based biomarkers comprising circulating tumor cells (CTCs), circulating cell-free nucleic acids or tumor-educated platelets is being tested in cancer patients. In this review we summarize the current state and clinical application of CTCs and circulating cell-free tumor DNA originating from blood as biomarkers in patients with different UCB stages.
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Affiliation(s)
- Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Armin Soave
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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83
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Chen L, Fu W, Zheng L, Liu Z, Liang G. Recent Progress of Small-Molecule Epidermal Growth Factor Receptor (EGFR) Inhibitors against C797S Resistance in Non-Small-Cell Lung Cancer. J Med Chem 2017; 61:4290-4300. [PMID: 29136465 DOI: 10.1021/acs.jmedchem.7b01310] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epidermal growth factor receptor (EGFR) has been a particular interest for drug development for treatment of non-small-cell lung cancer (NSCLC). The current third-generation EGFR small-molecule inhibitors, especially osimertinib, are at the forefront clinically for treatment of patients with NSCLC. However, a high percentage of these treated patients developed a tertiary cystein-797 to serine-790 (C797S) mutation in the EGFR kinase domain. This C797S mutation is thought to induce resistance to all current irreversible EGFR TKIs. In this Miniperspective, we present key mechanisms of resistance in response to third-generation EGFR TKIs, and emerging reports on novel EGFR TKIs to combat the resistance. Specifically, we analyze the allosteric and ATP-competitive inhibitors in terms of drug discovery, binding mechanism, and their potency and selectivity against EGFR harboring C797S mutations. Lastly, we provide some perspectives on new challenges and future directions in this field.
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Affiliation(s)
- Lingfeng Chen
- Chemical Biology Research Center at School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , China.,School of Chemical Engineering , Nanjing University of Science and Technology , Nanjing , Jiangsu 210094 , China
| | - Weitao Fu
- Chemical Biology Research Center at School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , China
| | - Lulu Zheng
- Chemical Biology Research Center at School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , China
| | - Zhiguo Liu
- Chemical Biology Research Center at School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , China
| | - Guang Liang
- Chemical Biology Research Center at School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , China.,School of Chemical Engineering , Nanjing University of Science and Technology , Nanjing , Jiangsu 210094 , China
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84
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Jambhekar N. Evolving concepts in lung cancer pathology and its impact on thoracic oncology practice. Indian J Thorac Cardiovasc Surg 2017. [DOI: 10.1007/s12055-017-0609-8] [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] Open
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85
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Lu CT, Zhang RM, Wang H, Kong FW, Wu WB, Gong LB, Zhang M. A rare case of cavitary lung cancer complicated with mycotic pneumonia and bullous emphysema: A case report and review of the literature. Medicine (Baltimore) 2017; 96:e8927. [PMID: 29382032 PMCID: PMC5709031 DOI: 10.1097/md.0000000000008927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE The accurate diagnosis and staging of cavitary lung cancer is challenging but essential for the choice of therapy; therefore, the differential diagnosis of cystic pulmonary lesions needs to be elucidated. PATIENT CONCERNS A patient was admitted with multifocal thin-walled cystic lesions in chest computed tomography. DIAGNOSES The patient had been diagnosed as heterogeneous bullous emphysema pathologically about 3 years ago. His diagnosis turned out to be metastatic cavitary lung cancer complicated with fungal pneumonia this time. INTERVENTIONS The patient underwent lung volume reduction surgery during his first hospitalization. Concurrent systemic chemotherapy and whole brain radiotherapy were administered after the diagnosis of cystic lung cancer. OUTCOMES The patient was lost to follow-up after the chemoradiotherapy. LESSONS Cavitary lung cancer should always be kept in mind during differential diagnosis of pulmonary cystic lesions. Pathological diagnosis by biopsy and surgery could be considered to avoid delayed treatment of malignancy.
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Affiliation(s)
- Cun-Tao Lu
- Department of General Thoracic Surgery, Xuzhou Central Hospital Affiliated to Southeast University
| | - Rui-Mei Zhang
- Department of Respiratory Medicine, Xuzhou Infectious Disease Hospital
| | - Heng Wang
- Department of General Thoracic Surgery, Xuzhou Central Hospital Affiliated to Southeast University
| | - Feng-Wei Kong
- Department of Respiratory Medicine, Xuzhou Infectious Disease Hospital
| | - Wen-Bin Wu
- Department of General Thoracic Surgery, Xuzhou Central Hospital Affiliated to Southeast University
| | - Long-Bo Gong
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital Affiliated to Southeast University, Xuzhou, China
| | - Miao Zhang
- Department of General Thoracic Surgery, Xuzhou Central Hospital Affiliated to Southeast University
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86
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Rave-Fränk M. Tumour-derived plasma cell-free DNA in patients with head and neck cancer: A short review. Cancer Radiother 2017; 21:554-556. [PMID: 28847459 DOI: 10.1016/j.canrad.2017.08.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Head and neck squamous cell carcinoma is one of the leading causes of cancer mortality worldwide. The prognosis for patients with head and neck squamous cell carcinoma has not substantially improved during the last decades, despite numerous advancements in treatment options. Reliable markers for early tumour detection and treatment response, which complement clinical examinations, imaging techniques, and biopsies would be extremely useful. One fairly new and promising method is the analysis of tumour-derived cell-free DNA (ctDNA) in the plasma of cancer patients. First data indicate that this method may assist, in the future, in the early detection of head and neck squamous cell carcinoma, the real-time monitoring of the disease course, the therapy response, and the prediction of prognosis with direct therapeutic implications by determining the best therapeutic modality for patient care.
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Affiliation(s)
- M Rave-Fränk
- Department of radiotherapy radiooncology, Universität Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany.
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