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Li A, Lou E, Leder K, Foo J. Early ctDNA kinetics as a dynamic biomarker of cancer treatment response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601508. [PMID: 39005329 PMCID: PMC11244961 DOI: 10.1101/2024.07.01.601508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Circulating tumor DNA assays are promising tools for the prediction of cancer treatment response. Here, we build a framework for the design of ctDNA biomarkers of therapy response that incorporate variations in ctDNA dynamics driven by specific treatment mechanisms. We develop mathematical models of ctDNA kinetics driven by tumor response to several therapy classes, and utilize them to simulate randomized virtual patient cohorts to test candidate biomarkers. Using this approach, we propose specific biomarkers, based on ctDNA longitudinal features, for targeted therapy, chemotherapy and radiation therapy. We evaluate and demonstrate the efficacy of these biomarkers in predicting treatment response within a randomized virtual patient cohort dataset. These biomarkers are based on novel proposals for ctDNA sampling protocols, consisting of frequent sampling within a compact time window surrounding therapy initiation - which we hypothesize to hold valuable prognostic information on longer-term treatment response. This study highlights a need for tailoring ctDNA sampling protocols and interpretation methodology to specific biological mechanisms of therapy response, and it provides a novel modeling and simulation framework for doing so. In addition, it highlights the potential of ctDNA assays for making early, rapid predictions of treatment response within the first days or weeks of treatment, and generates hypotheses for further clinical testing.
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Affiliation(s)
- Aaron Li
- School of Mathematics, University of Minnesota, Twin Cities, MN, USA
| | - Emil Lou
- Masonic Cancer Center, University of Minnesota, Twin Cities, MN, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, MN, USA
| | - Kevin Leder
- Department of Industrial and Systems Engineering, University of Minnesota, Twin Cities, MN, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Twin Cities, MN, USA
- Masonic Cancer Center, University of Minnesota, Twin Cities, MN, USA
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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3
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Thirty years of therapeutic innovation in melanoma research. Melanoma Res 2021; 31:105-107. [PMID: 33625105 DOI: 10.1097/cmr.0000000000000723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kozak K, Kowalik A, Gos A, Wasag B, Lugowska I, Jurkowska M, Krawczynska N, Kosela-Paterczyk H, Switaj T, Teterycz P, Klimczak A, Siedlecki JA, Chlopek M, Kalisz J, Limon J, Rutkowski P. Cell-free DNA BRAF V600E measurements during BRAF inhibitor therapy of metastatic melanoma: long-term analysis. TUMORI JOURNAL 2020; 106:300891619900928. [PMID: 32026754 DOI: 10.1177/0300891619900928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE We assessed the status of the BRAF V600E mutation in cell-free circulating tumor DNA (cfDNA) isolated from the plasma of patients with metastatic melanoma treated with the BRAF inhibitor vemurafenib, collected at different time points during therapy to evaluate the sensitivity and specificity of quantitative polymerase chain reaction and droplet digital polymerase chain reaction (ddPCR) and the correlation between the level of plasma cfDNA p.V600E and the long-term clinical outcome. METHODS cfDNA in patients with BRAF-mutated melanoma (n = 62) was analyzed at baseline and at 4-8 weeks from the start of vemurafenib therapy. BRAF mutations were assessed using tumor tissue-derived DNA and circulating cfDNA from plasma samples. Quantification of BRAF V600E was performed in cfDNA using ddPCR. RESULTS cfDNA V600E was detected in the plasma of 48/62 (77%) patients at baseline and in 18/62 (29%) patients after 4-8 weeks of treatment. Patients positive for BRAF mutations in cfDNA at baseline had shorter progression-free survival (PFS) and overall survival (OS) compared with patients with undetectable cfDNA BRAF mutations. Undetectable cfDNA p.V600E at baseline and after 4-8 weeks of therapy was associated with the best prognosis. When treated as a continuous variable, the log-transformed concentration of baseline cfDNA p.V600E was significantly associated with both PFS and OS. This effect was retained in the multivariate OS Cox model adjusted for Eastern Cooperative Oncology Group performance status, the presence of brain metastases, patient age, and previous systemic treatment. CONCLUSIONS Monitoring of plasma BRAF p.V600E cfDNA concentrations in patients with metastatic melanoma on targeted therapy may have prognostic value. Undetectable cfDNA p.V600E before and during treatment was associated with a favorable prognosis.
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Affiliation(s)
- Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Artur Kowalik
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Aleksandra Gos
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Bartosz Wasag
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | | | - Natalia Krawczynska
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Kosela-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Tomasz Switaj
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Paweł Teterycz
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Anna Klimczak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Małgorzata Chlopek
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Joanna Kalisz
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Janusz Limon
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
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Seremet T, Jansen Y, Planken S, Njimi H, Delaunoy M, El Housni H, Awada G, Schwarze JK, Keyaerts M, Everaert H, Lienard D, Del Marmol V, Heimann P, Neyns B. Undetectable circulating tumor DNA (ctDNA) levels correlate with favorable outcome in metastatic melanoma patients treated with anti-PD1 therapy. J Transl Med 2019; 17:303. [PMID: 31488153 PMCID: PMC6727487 DOI: 10.1186/s12967-019-2051-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 08/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Treatment with anti-PD1 monoclonal antibodies improves the survival of metastatic melanoma patients but only a subgroup of patients benefits from durable disease control. Predictive biomarkers for durable benefit could improve the clinical management of patients. METHODS Plasma samples were collected from patients receiving anti-PD1 therapy for ctDNA quantitative assessment of BRAFV600 and NRASQ61/G12/G13 mutations. RESULTS After a median follow-up of 84 weeks 457 samples from 85 patients were analyzed. Patients with undetectable ctDNA at baseline had a better PFS (Hazard ratio (HR) = 0.47, median 26 weeks versus 9 weeks, p = 0.01) and OS (HR = 0.37, median not reached versus 21.3 weeks, p = 0.005) than patients with detectable ctDNA. Additionally, the HR for death was lower after the ctDNA level became undetectable during follow-up (adjusted HR: 0.16 (95% CI 0.07-0.36), p-value < 0.001). ctDNA levels > 500 copies/ml at baseline or week 3 were associated with poor clinical outcome. Patients progressive exclusively in the central nervous system (CNS) had undetectable ctDNA at baseline and at subsequent assessments. In multivariate analysis adjusted for LDH, CRP, ECOG and number of metastatic sites, the ctDNA remained significant for PFS and OS. A positive correlation was observed between ctDNA levels and total metabolic tumor volume (TMTV), number of metastatic sites and total tumor burden. CONCLUSIONS Assessment of ctDNA baseline and during therapy was predictive for tumor response and clinical outcome in metastatic melanoma patients and reflected the tumor burden. ctDNA evaluation provided reliable complementary information during anti-PD1 antibody therapy.
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Affiliation(s)
- Teofila Seremet
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
- Department of Dermatology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yanina Jansen
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Simon Planken
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Hassan Njimi
- Department of Biomedical Statistics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mélanie Delaunoy
- Laboratory of Molecular Biology in Haemato-oncology, LHUB-ULB, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Hakim El Housni
- Laboratory of Molecular Biology in Haemato-oncology, LHUB-ULB, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gil Awada
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Julia Katharina Schwarze
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Marleen Keyaerts
- Department of Nuclear Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hendrik Everaert
- Department of Nuclear Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Danielle Lienard
- Department of Dermatology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Véronique Del Marmol
- Department of Dermatology, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pierre Heimann
- Laboratory of Molecular Biology in Haemato-oncology, LHUB-ULB, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bart Neyns
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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Tarhini A, Kudchadkar RR. Predictive and on-treatment monitoring biomarkers in advanced melanoma: Moving toward personalized medicine. Cancer Treat Rev 2018; 71:8-18. [DOI: 10.1016/j.ctrv.2018.09.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/16/2022]
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7
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Long-Mira E, Ilie M, Chamorey E, Leduff-Blanc F, Montaudié H, Tanga V, Allégra M, Lespinet-Fabre V, Bordone O, Bonnetaud C, Schiappa R, Butori C, Bence C, Lacour JP, Hofman V, Hofman P. Monitoring BRAF and NRAS mutations with cell-free circulating tumor DNA from metastatic melanoma patients. Oncotarget 2018; 9:36238-36249. [PMID: 30546839 PMCID: PMC6281416 DOI: 10.18632/oncotarget.26343] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 01/05/2023] Open
Abstract
The mutation status of the BRAF and NRAS genes in tumor tissue is used to select patients with metastatic melanoma for targeted therapy. Cell-free circulating DNA (cfDNA) represents an accessible, non-invasive surrogate sample that could provide a snapshot of the BRAF and NRAS genotype in these patients. We investigated the feasibility of the Idylla™ assay for detection of BRAF and NRAS mutations in cfDNA of 19 patients with metastatic melanoma at baseline and during the course of treatment. The cfDNA genotype obtained with Idylla was compared to the results obtained with matched-tumor tissue and to clinical outcome. At baseline, 47% of patients harbored a BRAFV600 mutation in their cfDNA. Two months after targeted treatment the BRAFV600 mutant cfDNA was undetectable in all patients and 3 were disease-free. Moreover, 15% of patients harbored a NRAS mutation that was detected with plasma before treatment. The sensitivity and specificity were 80% and 89% for the BRAF status, and 79% and 100% for the NRAS status in pretreatment cfDNA compared to results obtained with a tissue test. Due to the small size of the population, no significant correlation was observed between the presence of BRAF or NRAS mutations in cfDNA and the metastatic tumor load or overall survival. In conclusion, this study demonstrated that evaluation with the Idylla system of the BRAF and NRAS mutation status in cfDNA may be a surrogate for determination of the BRAF and NRAS status in tumor tissue.
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Affiliation(s)
- Elodie Long-Mira
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Team 4, Nice, France
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Marius Ilie
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Team 4, Nice, France
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Emmanuel Chamorey
- Antoine Lacassagne Comprehensive Cancer Center, FHU OncoAge, Biostatistics Unit, Nice, France
| | - Florence Leduff-Blanc
- Université Côte d'Azur, CHU Nice, Department of Dermatology, Archet Hospital, Nice, France
| | - Henri Montaudié
- Université Côte d'Azur, CHU Nice, Department of Dermatology, Archet Hospital, Nice, France
| | - Virginie Tanga
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Maryline Allégra
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | | | - Olivier Bordone
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Christelle Bonnetaud
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Renaud Schiappa
- Antoine Lacassagne Comprehensive Cancer Center, FHU OncoAge, Biostatistics Unit, Nice, France
| | - Catherine Butori
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
| | - Coraline Bence
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
| | - Jean-Philippe Lacour
- Université Côte d'Azur, CHU Nice, Department of Dermatology, Archet Hospital, Nice, France
| | - Véronique Hofman
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Team 4, Nice, France
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
| | - Paul Hofman
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Team 4, Nice, France
- Université Côte d'Azur, CHU Nice, FHU OncoAge, Hospital-Integrated Biobank, Nice, France
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Illustrative cases for monitoring by quantitative analysis of BRAF/NRAS ctDNA mutations in liquid biopsies of metastatic melanoma patients who gained clinical benefits from anti-PD1 antibody therapy. Melanoma Res 2018; 28:65-70. [PMID: 29227333 DOI: 10.1097/cmr.0000000000000415] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Anti-programmed death 1 (PD-1) monoclonal antibodies improve the survival of metastatic melanoma patients. Predictive or monitoring biomarkers for response to this therapy could improve the clinical management of these patients. To date, no established biomarkers are available for monitoring the response to immunotherapy. Tumor- specific mutations in circulating tumor DNA (ctDNA) such as BRAF and NRAS mutations for melanoma patients have been proposed for monitoring of immunotherapy response. We present seven illustrative cases for the use of ctDNA BRAF and NRAS mutations' monitoring in plasma. The cases described exemplify four distinct clinical benefit patterns: rapid and durable complete response (CR), early progression, followed by CR, CR followed by early progression after interrupting treatment and long-term disease stabilization. These representative cases suggest that comprehensive BRAF/NRAS ctDNA monitoring during anti-PD1 therapy is informative and can be of added value for the monitoring of melanoma patients gaining clinical benefit on anti-PD1 treatment. An important advantage of our approach is that using the cartridge system on the Idylla platform for mutation analysis, the results become available the same day 2 h after plasma collection. Therefore, in the future, the ctDNA level can be an element in the clinical management of the patients.
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Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma. Pigment Cell Melanoma Res 2018; 31:73-81. [PMID: 28786531 PMCID: PMC5742050 DOI: 10.1111/pcmr.12623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.
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Affiliation(s)
- Tara C. Gangadhar
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha L. Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wei Xu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Alexander C. Huang
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institue for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Parker Institute of Immunotherapy at the University of Pennsylvania
| | - Shannon Harmon
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Devon Soucier
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ravi K. Amaravadi
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lynn M. Schuchter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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10
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Chang Y, Tolani B, Nie X, Zhi X, Hu M, He B. Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring. Ther Clin Risk Manag 2017; 13:1363-1374. [PMID: 29066904 PMCID: PMC5644666 DOI: 10.2147/tcrm.s141991] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.
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Affiliation(s)
- Yi Chang
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Xiuhong Nie
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiuyi Zhi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Mu Hu
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Biao He
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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11
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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13
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Abstract
Malignant melanoma remains the skin cancer with the highest number of mortalities worldwide. While early diagnosis and complete surgical excision remain the best possibility for curing disease, prognosis at the stage of metastasis is still poor. Recent years have brought about considerable advances in terms of understanding the pathogenesis of melanoma and treating advanced disease. The discovery of activating BRAF mutations in around 50% of tumors has led to the introduction of targeted therapies downregulating BRAF signaling output. These have been further refined as combination therapies, which by targeting multiple targets have further improved the clinical outcome. A comparable, potentially even superior therapeutic alternative has been the introduction of immunotherapeutic approaches, including PD-1 and CTLA-4 checkpoint blockade therapies. Despite all genetic knowledge acquired in recent years, a clearly applicable prognostic signature of clinical value has not been established. General prognostic assessment of cutaneous melanoma remains based on clinical and pathological criteria (most importantly tumor thickness). The main challenges lying ahead are to establish a reliable prognostic test effectively determining which tumors will metastasize. Additionally establishing biomarkers which will allow patients to be stratified according to the most promising systemic therapy (immunotherapies and/or BRAF inhibitor therapies) is of utmost importance for patients with metastasized disease. Identifying serum biomarkers enabling disease to be monitored as well as determining tumor properties (i.e. resistance) would also be of great value. While initial results have proven promising, there remains much work to be done.
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Affiliation(s)
- Klaus G Griewank
- a Department of Dermatology , University Hospital Essen , Essen , Germany
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Schreuer M, Meersseman G, Van Den Herrewegen S, Jansen Y, Chevolet I, Bott A, Wilgenhof S, Seremet T, Jacobs B, Buyl R, Maertens G, Neyns B. Quantitative assessment of BRAF V600 mutant circulating cell-free tumor DNA as a tool for therapeutic monitoring in metastatic melanoma patients treated with BRAF/MEK inhibitors. J Transl Med 2016; 14:95. [PMID: 27095081 PMCID: PMC4837559 DOI: 10.1186/s12967-016-0852-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND BRAF V600 mutant circulating cell-free tumor DNA (BRAF V600mut ctDNA) could serve as a specific biomarker in patients with BRAF V600 mutant melanoma. We analyzed the value of BRAF V600mut ctDNA from plasma as a monitoring tool for advanced melanoma patients treated with BRAF/MEK inhibitors. METHODS Allele-specific quantitative PCR analysis for BRAF V600 E/E2/D/K/R/M mutations was performed on DNA extracted from plasma of patients with known BRAF V600 mutant melanoma who were treated with dabrafenib and trametinib. RESULTS 245 plasma samples from 36 patients were analyzed. In 16 patients the first plasma sample was obtained before the first dosing of dabrafenib/trametinib. At baseline, BRAF V600mut ctDNA was detected in 75 % of patients (n = 12/16). BRAF V600mut ctDNA decreased rapidly upon initiation of targeted therapy (p < 0.001) and became undetectable in 60 % of patients (n = 7/12) after 6 weeks of treatment. During treatment, disease progression (PD) was diagnosed in 27 of 36 patients. An increase of the BRAF V600mut ctDNA copy number and fraction, identified PD with a sensitivity of 70 % (n = 19/27) and a specificity of 100 %. An increase in the BRAF V600mut ctDNA fraction was detected prior to clinical PD in 44 % of cases (n = 12/27) and simultaneously with PD in 26 % of patients (n = 7/27). CONCLUSIONS Quantitative analysis of BRAF V600mut ctDNA in plasma has unique features as a monitoring tool during treatment with BRAF/MEK inhibitors. Its potential as an early predictor of acquired resistance deserves further evaluation.
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Affiliation(s)
- Max Schreuer
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Geert Meersseman
- />Biocartis, Generaal De Wittelaan 11 B3, 2800 Mechelen, Belgium
| | | | - Yanina Jansen
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ines Chevolet
- />Department of Dermatology, Universitair ziekenhuis Gent (UZ Gent), Universiteit Gent (UGent), De Pintelaan 185, 9000 Ghent, Belgium
| | - Ambre Bott
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Sofie Wilgenhof
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Teofila Seremet
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Bart Jacobs
- />Biocartis, Generaal De Wittelaan 11 B3, 2800 Mechelen, Belgium
| | - Ronald Buyl
- />Department of Biostatistics and Medical Informatics, Vrije Universiteit Brussel (VUB), Laarbeeklaan, 103, 1090 Brussels, Belgium
| | - Geert Maertens
- />Biocartis, Generaal De Wittelaan 11 B3, 2800 Mechelen, Belgium
| | - Bart Neyns
- />Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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15
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Ashida A, Sakaizawa K, Mikoshiba A, Uhara H, Okuyama R. Quantitative analysis of the BRAF V600E mutation in circulating tumor-derived DNA in melanoma patients using competitive allele-specific TaqMan PCR. Int J Clin Oncol 2016; 21:981-988. [PMID: 27041702 DOI: 10.1007/s10147-016-0976-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND BRAF V600E is a common mutation in melanoma, and BRAF inhibitors are effective in treating of BRAF mutation-positive melanoma. DNA carrying this mutation is released from melanoma cells into the circulation. As such, circulating tumor-derived DNA (ctDNA) in peripheral blood represents a novel biomarker for evaluating tumor features in cancer patients. However, ctDNA is present in the peripheral blood at very low levels, which makes the detection of specific mutations in this DNA a challenge. Competitive allele-specific TaqMan PCR (castPCR), a straightforward commercially available assay, is a sensitive technique for quantitating a small amount of DNA. METHODS The level of BRAF V600E ctDNA was quantified by castPCR in 26 consecutive plasma samples from six melanoma patients. RESULTS The castPCR assay was performed using a mixture of BRAF V600E DNA and BRAF wild DNA and found to be able to detect BRAF V600E at a fractional abundance of ≥0.5 % in 2- to 10-ng samples of genomic DNA. Cell-free DNA was then extracted from peripheral blood samples collected from six patients with melanoma harboring the BRAF V600E mutation. BRAF V600E ctDNA was detected in three patients, at a fractional abundance of between 1.28 and 58.0 % of total BRAF cell-free DNA. The abundance of BRAF V600E ctDNA correlated with tumor burden, as determined by computed tomography imaging. In two cases, an increase in the level of BRAF V600E ctDNA preceded exacerbation of clinical symptoms. CONCLUSION The castPCR assay can detect and quantitate small amounts of BRAF V600E ctDNA in samples containing large amounts of BRAF wild cell-free DNA. Thus, we suggest that the castPCR assay is suitable for monitoring ctDNA in the plasma of melanoma patients.
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Affiliation(s)
- Atsuko Ashida
- Department of Dermatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Kaori Sakaizawa
- Department of Dermatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Asuka Mikoshiba
- Department of Dermatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Hisashi Uhara
- Department of Dermatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Ryuhei Okuyama
- Department of Dermatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
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