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Stormoen DR, Rohrberg KS, Mouw KW, Ørum K, Szallasi Z, Rossing M, Bagger FO, Pappot H. Similar genetic profile in early and late stage urothelial tract cancer. J Cancer Res Clin Oncol 2024; 150:339. [PMID: 38976041 PMCID: PMC11230994 DOI: 10.1007/s00432-024-05850-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/14/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Urothelial tract cancer (UTC) ranks as the tenth most prevalent cancer and holds the seventh position in terms of mortality worldwide. Despite its prevalence and mortality ranking, there are still gaps in the knowledge of the mutational landscape in patients with advanced disease who have limited therapeutic options after multiple lines of prior treatment. This study compares the genomic and transcriptomic landscape, and targeted treatment options between metastatic UTC (mUTC) patients treated with multiple lines of therapy compared to newly diagnosed, untreated Muscle Invasive Bladder Cancer (MIBC). METHODS We compared genomic and clinical data from two cohorts: mUTC patients who received multiple lines of therapy and were referred to the Copenhagen Prospective Personalized Oncology (CoPPO) project at Rigshospitalet, University of Copenhagen. Data for MIBC UTC patients were acquired from the Cancer Genome Atlas Bladder Cancer (TCGA BLCA) cohort. Biopsies in CoPPO were performed at the time of enrollment. 523 highly important cancer-related genes (TrueSight Oncology-500 targeted sequencing panel) were used from both cohorts for comparative analysis. Analyses included RNA count data to compare predicted molecular subtypes in each cohort separately. RESULTS Patients from the CoPPO cohort had a lower median age at first-line treatment than the TCGA BLCA cohort, with no significant gender disparity. The predominant histology was urothelial cell carcinoma in both cohorts. Genomic analysis revealed no significant difference between the top mutated genes in the two cohorts, specifically looking into DNA damage repair genes. Molecular subtyping indicated a higher frequency of neuroendocrine differentiation in the CoPPO cohort. 13% of patients in the CoPPO cohort received targeted therapy based on genomic findings, and 16% received non-targeted treatment, totaling 29% receiving CoPPO treatment (9 patients). The remaining 71% received best supportive care. Kaplan-Meier analysis showed a non-significant survival benefit for the intervention group in the CoPPO cohort. CONCLUSION When focusing on 523 highly relevant cancer genes, the mutational profile of mUTC patients who have undergone numerous treatment lines resembles that of newly diagnosed MIBC. These alterations can be targeted, indicating the potential advantage of early genomic testing for personalized treatment within clinical trials.
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Affiliation(s)
- Dag Rune Stormoen
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Kristoffer Staal Rohrberg
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kent William Mouw
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katrine Ørum
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
| | - Zoltan Szallasi
- Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Translational Cancer Genomics Group, Danish Cancer Society, Copenhagen, Denmark
| | - Maria Rossing
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Department for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Helle Pappot
- Department of Oncology, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen, 5073, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Kringelbach T, Højgaard M, Rohrberg K, Spanggaard I, Laursen BE, Ladekarl M, Haslund CA, Harsløf L, Belcaid L, Gehl J, Søndergaard L, Eefsen RL, Hansen KH, Kodahl AR, Jensen LH, Holt MI, Oellegaard TH, Yde CW, Ahlborn LB, Lassen U. ProTarget: a Danish Nationwide Clinical Trial on Targeted Cancer Treatment based on genomic profiling - a national, phase 2, prospective, multi-drug, non-randomized, open-label basket trial. BMC Cancer 2023; 23:182. [PMID: 36814246 PMCID: PMC9948467 DOI: 10.1186/s12885-023-10632-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND An increasing number of trials indicate that treatment outcomes in cancer patients with metastatic disease are improved when targeted treatments are matched with druggable genomic alterations in individual patients (pts). An estimated 30-80% of advanced solid tumors harbor actionable genomic alterations. However, the efficacy of personalized cancer treatment is still scarcely investigated in larger, controlled trials due to the low frequency and heterogenous distribution of druggable alterations among different histologic tumor types. Therefore, the overall effect of targeted cancer treatment on clinical outcomes still needs investigation. STUDY DESIGN/METHODS ProTarget is a national, non-randomized, multi-drug, open-label, pan-cancer phase 2 trial aiming to investigate the anti-tumor activity and toxicity of currently 13 commercially available, EMA-approved targeted therapies outside the labeled indication for treatment of advanced malignant diseases, harboring specific actionable genomic alterations. The trial involves the Danish National Molecular Tumor Board for confirmation of drug-variant matches. Key inclusion criteria include a) measurable disease (RECIST v.1.1), b) ECOG performance status 0-2, and c) an actionable genomic alteration matching one of the study drugs. Key exclusion criteria include a) cancer type within the EMA-approved label of the selected drug, and b) genomic alterations known to confer drug resistance. Initial drug dose, schedule and dose modifications are according to the EMA-approved label. The primary endpoint is objective response or stable disease at 16 weeks. Pts are assigned to cohorts defined by the selected drug, genomic alteration, and tumor histology type. Cohorts are monitored according to a Simon's two-stage-based design. Response is assessed every 8 weeks for the first 24 weeks, then every 12 weeks. The trial is designed similar to the Dutch DRUP and the ASCO TAPUR trials and is a partner in the Nordic Precision Cancer Medicine Trial Network. In ProTarget, serial fresh tumor and liquid biopsies are mandatory and collected for extensive translational research including whole genome sequencing, array analysis, and RNA sequencing. DISCUSSION The ProTarget trial will identify new predictive biomarkers for targeted treatments and provide new data and essential insights in molecular pathways involved in e.g., resistance mechanisms and thereby potentially evolve and expand the personalized cancer treatment strategy. PROTOCOL VERSION 16, 09-MAY-2022. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04341181. Secondary Identifying No: ML41742. EudraCT No: 2019-004771-40.
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Affiliation(s)
- Tina Kringelbach
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Martin Højgaard
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Iben Spanggaard
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Britt Elmedal Laursen
- grid.7048.b0000 0001 1956 2722Department of Molecular Medicine/Department of Oncology, Aarhus University Hospital, and Institute of Biomedicine, Pharmacology/Precision Medicine, Aarhus University, Aarhus, Denmark
| | - Morten Ladekarl
- grid.27530.330000 0004 0646 7349Department of Oncology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Charlotte Aaquist Haslund
- grid.27530.330000 0004 0646 7349Department of Oncology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Laurine Harsløf
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Laila Belcaid
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Julie Gehl
- grid.476266.7Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Søndergaard
- grid.476266.7Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark
| | | | - Karin Holmskov Hansen
- grid.7143.10000 0004 0512 5013Department of Oncology, Clinic of Precision Medicine, Odense University Hospital, Odense, Denmark
| | - Annette Raskov Kodahl
- grid.7143.10000 0004 0512 5013Department of Oncology, Clinic of Precision Medicine, Odense University Hospital, Odense, Denmark ,grid.10825.3e0000 0001 0728 0170Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Henrik Jensen
- grid.417271.60000 0004 0512 5814Department of Oncology, Vejle Hospital and University Hospital of Southern Denmark, Vejle, Denmark
| | - Marianne Ingerslev Holt
- grid.417271.60000 0004 0512 5814Department of Clinical Genetics, Vejle Hospital and University Hospital of Southern Denmark, Vejle, Denmark
| | - Trine Heide Oellegaard
- grid.7048.b0000 0001 1956 2722Department of Oncology, Goedstrup Hospital, Goedstrup, and Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Ulrik Lassen
- Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark.
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Fernandes MGO, Sousa C, Pereira Reis J, Cruz-Martins N, Souto Moura C, Guimarães S, Justino A, Pina MJ, Magalhães A, Queiroga H, Marques JA, Machado JC, Costa JL, Hespanhol V. Liquid Biopsy for Disease Monitoring in Non-Small Cell Lung Cancer: The Link between Biology and the Clinic. Cells 2021; 10:cells10081912. [PMID: 34440680 PMCID: PMC8394732 DOI: 10.3390/cells10081912] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Cell-free DNA (cfDNA) analysis offers a non-invasive method to identify sensitising and resistance mutations in advanced Non-Small Cell Lung Cancer (NSCLC) patients. Next-generation sequencing (NGS) of circulating free DNA (cfDNA) is a valuable tool for mutations detection and disease's clonal monitoring. MATERIAL AND METHODS An amplicon-based targeted gene NGS panel was used to analyse 101 plasma samples of advanced non-small cell lung cancer (NSCLC) patients with known oncogenic mutations, mostly EGFR mutations, serially collected at different clinically relevant time points of the disease. RESULTS The variant allelic frequency (VAF) monitoring in consecutive plasma samples demonstrated different molecular response and progression patterns. The decrease in or the clearance of the mutant alleles was associated with response and the increase in or the emergence of novel alterations with progression. At the best response, the median VAF was 0% (0.0% to 3.62%), lower than that at baseline, with a median of 0.53% (0.0% to 9.9%) (p = 0.004). At progression, the VAF was significantly higher (median 4.67; range: 0.0-36.9%) than that observed at the best response (p = 0.001) and baseline (p = 0.006). These variations anticipated radiographic changes in most cases, with a median time of 0.86 months. Overall, the VAF evolution of different oncogenic mutations predicts clinical outcomes. CONCLUSION The targeted NGS of circulating tumour DNA (ctDNA) has clinical utility to monitor treatment response in patients with advanced lung adenocarcinoma.
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Affiliation(s)
- Maria Gabriela O. Fernandes
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Correspondence: ; Tel.: +351-96-574-4014
| | - Catarina Sousa
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
| | - Joana Pereira Reis
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Conceição Souto Moura
- Pathology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
| | - Susana Guimarães
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Pathology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
| | - Ana Justino
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Maria João Pina
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Adriana Magalhães
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
| | - Henrique Queiroga
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
| | - José Agostinho Marques
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
| | - José Carlos Machado
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - José Luís Costa
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
| | - Venceslau Hespanhol
- Pulmonology Department, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.); (A.M.); (H.Q.); (J.A.M.); (V.H.)
- Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal; (N.C.-M.); (S.G.); (J.C.M.); (J.L.C.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal; (J.P.R.); (A.J.); (M.J.P.)
- Institute for Research and Innovation in Health (i3S), University of Porto, Rua Alfredo Allen, 4200-135 Porto, Portugal
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Roviello G, D'Angelo A, Sirico M, Pittacolo M, Conter FU, Sobhani N. Advances in anti-BRAF therapies for lung cancer. Invest New Drugs 2021; 39:879-890. [PMID: 33474634 PMCID: PMC8068629 DOI: 10.1007/s10637-021-01068-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/14/2021] [Indexed: 12/14/2022]
Abstract
Non-small cell lung cancer (NSCLC) is one of the most frequent causes of mortality in the western world. v-raf murine sarcoma viral oncogene homolog B (BRAF) is a member of the Raf kinase family and plays a critical role in cellular growth, proliferation, and differentiation through the mitogen-activated protein kinase pathway. The incidence of BRAF mutations in NSCLC is low, accounting for 0-3% of all cases of lung cancer. Given the results obtained in metastatic melanoma, several studies have reported the efficacy of anti-BRAF therapies in NSCLC treatment. In this review, we describe changes in the landscape of BRAF-mutated lung cancer treatment and analyze insights from major clinical trials in the context of future therapeutic prospects.
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Affiliation(s)
- Giandomenico Roviello
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, viale Pieraccini, 6, 50139, Florence, Italy.
| | - Alberto D'Angelo
- Department of Biology & Biochemistry, University of Bath, Bath, BA2-7AX, UK
| | - Marianna Sirico
- Multidisciplinary Operative Unit of Mammary Pathology and Translational Research, ASST of Cremona, 26100, Cremona, Italy
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Matteo Pittacolo
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Felipe Umpierre Conter
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Navid Sobhani
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
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Gill AB, Rundo L, Wan JCM, Lau D, Zawaideh JP, Woitek R, Zaccagna F, Beer L, Gale D, Sala E, Couturier DL, Corrie PG, Rosenfeld N, Gallagher FA. Correlating Radiomic Features of Heterogeneity on CT with Circulating Tumor DNA in Metastatic Melanoma. Cancers (Basel) 2020; 12:E3493. [PMID: 33255267 PMCID: PMC7759931 DOI: 10.3390/cancers12123493] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Clinical imaging methods, such as computed tomography (CT), are used for routine tumor response monitoring. Imaging can also reveal intratumoral, intermetastatic, and interpatient heterogeneity, which can be quantified using radiomics. Circulating tumor DNA (ctDNA) in the plasma is a sensitive and specific biomarker for response monitoring. Here we evaluated the interrelationship between circulating tumor DNA mutant allele fraction (ctDNAmaf), obtained by targeted amplicon sequencing and shallow whole genome sequencing, and radiomic measurements of CT heterogeneity in patients with stage IV melanoma. ctDNAmaf and radiomic observations were obtained from 15 patients with a total of 70 CT examinations acquired as part of a prospective trial. 26 of 39 radiomic features showed a significant relationship with log(ctDNAmaf). Principal component analysis was used to define a radiomics signature that predicted ctDNAmaf independent of lesion volume. This radiomics signature and serum lactate dehydrogenase were independent predictors of ctDNAmaf. Together, these results suggest that radiomic features and ctDNAmaf may serve as complementary clinical tools for treatment monitoring.
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Affiliation(s)
- Andrew B. Gill
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
- Imaging Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
| | - Jonathan C. M. Wan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; (J.C.M.W.); (D.-L.C.)
| | - Doreen Lau
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
| | - Jeries P. Zawaideh
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
| | - Ramona Woitek
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
| | - Fulvio Zaccagna
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
| | - Lucian Beer
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
| | - Davina Gale
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; (J.C.M.W.); (D.-L.C.)
| | - Evis Sala
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
| | - Dominique-Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; (J.C.M.W.); (D.-L.C.)
| | - Pippa G. Corrie
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; (J.C.M.W.); (D.-L.C.)
| | - Ferdia A. Gallagher
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (L.R.); (D.L.); (J.P.Z.); (R.W.); (F.Z.); (L.B.); (E.S.); (F.A.G.)
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0RE, UK; (D.G.); (N.R.)
- Imaging Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
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Quantitative analysis of the BRAF V595E mutation in plasma cell-free DNA from dogs with urothelial carcinoma. PLoS One 2020; 15:e0232365. [PMID: 32330187 PMCID: PMC7182225 DOI: 10.1371/journal.pone.0232365] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/13/2020] [Indexed: 11/19/2022] Open
Abstract
Circulating tumor DNA (ctDNA), which carries tumor-specific mutations, is an emerging candidate biomarker for malignancies and for monitoring disease status in various human tumors. Recently, BRAF V595E mutation has been reported in 80% of dogs with urothelial carcinoma. This study investigates the BRAF V595E allele concentration in circulating cell-free DNA (cfDNA) and assesses the clinical significance of BRAF-mutated ctDNA levels in canines with urothelial carcinoma. A total of 15 dogs with urothelial carcinoma were included. cfDNA concentration was measured using a real-time polymerase chain reaction (PCR) of the LINE-1 gene. To measure the concentration of the mutated BRAF gene in cfDNA, allele-specific real-time PCR with a locked nucleic acid probe was performed. BRAF mutations were detected in 11 (73%) of the 15 tested tumor samples. BRAF-mutated ctDNA concentrations were significantly higher in dogs with the BRAF mutation (14.05 ± 13.51 ng/ml) than in wild-type dogs (0.21 ± 0.41 ng/ml) (p = 0.031). The amount of BRAF-mutated ctDNA in plasma increased with disease progression and responded to treatment. Our results show that BRAF-mutated ctDNA can be detected using allele-specific real-time PCR in plasma samples of canines with urothelial carcinoma with the BRAF V595E mutation. This ctDNA analysis may be a potentially useful tool for monitoring the progression of urothelial carcinoma and its response to treatment.
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Greytak SR, Engel KB, Parpart-Li S, Murtaza M, Bronkhorst AJ, Pertile MD, Moore HM. Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance. Clin Cancer Res 2020; 26:3104-3109. [PMID: 32122922 DOI: 10.1158/1078-0432.ccr-19-3015] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/25/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.
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Affiliation(s)
| | | | | | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Mark D Pertile
- Victorian Clinical Genetics Services (VCGS), Parkville, Australia
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, NCI, Bethesda, Maryland.
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8
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Bos MK, Angus L, Nasserinejad K, Jager A, Jansen MPHM, Martens JWM, Sleijfer S. Whole exome sequencing of cell-free DNA - A systematic review and Bayesian individual patient data meta-analysis. Cancer Treat Rev 2019; 83:101951. [PMID: 31874446 DOI: 10.1016/j.ctrv.2019.101951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/21/2022]
Abstract
Molecular profiling of tumor derived cell free DNA (cfDNA) is gaining ground as a prognostic and predictive biomarker. However to what extent cfDNA reflects the full metastatic landscape as currently determined by tumor tissue analysis remains controversial. Though technically challenging, whole exome sequencing (WES) of cfDNA enables thorough evaluation of somatic alterations. Here, we review the feasibility of WES of cfDNA and determine the sensitivity of WES-detected single nucleotide variants (SNVs) in cfDNA on individual patient data level using paired tumor tissue as reference (sharedSNVsAlltissueSNVs×100%). The pooled sensitivity was 50% (95% credible interval (CI): 29-72%). The tissue mutant allele frequency (MAF) of variants exclusively identified in tissue was significantly lower (12.5%, range: 0.5-18%) than the tissue MAF of variants identified in both tissue and cfDNA (23.9%, range: 17-38%), p = 0.004. The overall agreement (sharedSNVsAllSNVs×100%)between SNVs in cfDNA and tumor tissue was 31% (95% CI: 15-49%). The number of detected SNVs was positively correlated with circulating tumor DNA (ctDNA) fraction (p = 0.016). A sub analysis of samples with ctDNA fractions ≥ 25% improved the sensitivity to 69% (95% CI: 46-89%) and agreement to 46% (95% CI: 36-59%), suggesting that WES is mainly feasible for patients with high ctDNA fractions. Pre- and post-analytical procedures were highly variable between studies rendering comparisons problematic. In conclusion, various aspects of WES of cfDNA are largely in its investigative phase, standardization of methodologies is highly needed to bring this promising technique to its clinical potential.
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Affiliation(s)
- Manouk K Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Kazem Nasserinejad
- HOVON Data Center, Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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9
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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: 49] [Impact Index Per Article: 9.8] [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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10
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Nørøxe DS, Østrup O, Yde CW, Ahlborn LB, Nielsen FC, Michaelsen SR, Larsen VA, Skjøth-Rasmussen J, Brennum J, Hamerlik P, Poulsen HS, Lassen U. Cell-free DNA in newly diagnosed patients with glioblastoma - a clinical prospective feasibility study. Oncotarget 2019; 10:4397-4406. [PMID: 31320993 PMCID: PMC6633897 DOI: 10.18632/oncotarget.27030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Glioblastoma (GB) is an incurable brain cancer with limited treatment options. The aim was to test the feasibility of using cell-free DNA (cfDNA) to support evaluation of treatment response, pseudo-progression and whether progression could be found before clinical and/or radiologic progression.
Results: CfDNA fluctuated during treatment with the highest levels before diagnostic surgery and at progression. An increase was seen in 3 out of 4 patients at the time of progression while no increase was seen in 3 out of 4 patients without progression. CfDNA levels could aid in 3 out of 3 questionable cases of pseudo-progression.
Methods: Eight newly diagnosed GB patients were included. Blood samples were collected prior to diagnosis, before start and during oncologic treatment until progression. Seven patients received concurrent radiotherapy/Temozolomide with adjuvant Temozolomide with one of the patients included in a clinical trial with either immunotherapy or placebo as add-on. One patient received radiation alone. CfDNA concentration was determined for each blood sample.
Conclusions: It was feasible to measure cfDNA concentration. Despite the limited cohort size, there was a good tendency between cfDNA and treatment course and -response, respectively with the highest levels at progression.
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Affiliation(s)
- Dorte Schou Nørøxe
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | | | | | | | | | - Jannick Brennum
- Department of Neurosurgery, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Ulrik Lassen
- Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
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11
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Donnelly D, Aung PP, Jour G. The "-OMICS" facet of melanoma: Heterogeneity of genomic, proteomic and metabolomic biomarkers. Semin Cancer Biol 2019; 59:165-174. [PMID: 31295564 DOI: 10.1016/j.semcancer.2019.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023]
Abstract
In the recent decade, cutting edge molecular and proteomic analysis platforms revolutionized biomarkers discovery in cancers. Melanoma is the prototype with over 51,100 biomarkers discovered and investigated thus far. These biomarkers include tissue based tumor cell and tumor microenvironment biomarkers and circulating biomarkers including tumor DNA (cf-DNA), mir-RNA, proteins and metabolites. These biomarkers provide invaluable information for diagnosis, prognosis and play an important role in prediction of treatment response. In this review, we summarize the most recent discoveries in each of these biomarker categories. We will discuss the challenges in their implementation and standardization and conclude with some perspectives in melanoma biomarker research.
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Affiliation(s)
- Douglas Donnelly
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, United States; Interdisciplinary Melanoma Program, New York University School of Medicine, New York, NY, United States
| | - Phyu P Aung
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - George Jour
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, United States; Interdisciplinary Melanoma Program, New York University School of Medicine, New York, NY, United States; Department of Pathology, New York University School of Medicine, New York, NY, United States.
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12
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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13
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Barlebo Ahlborn L, Østrup O. Toward liquid biopsies in cancer treatment: application of circulating tumor DNA. APMIS 2019; 127:329-336. [PMID: 30784124 DOI: 10.1111/apm.12912] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 12/13/2022]
Abstract
Circulating tumor DNA (ctDNA) refers to the fraction of cell-free DNA in a patient's blood originating from tumor cells. Increased knowledge about tumor genomics, improvements in targeted therapies, and accompanying advances in DNA-sequencing technologies have increased the interest in using ctDNA as a minimally invasive tool in cancer diagnostics and treatment. Especially, early tumor detection including identification of minimal residual disease and stratification of adjuvant therapy are promising approaches. Also, ctDNA showed to be reliable in treatment monitoring and can be used to assess therapy resistance due to the broad variety of tumor subclones captured in ctDNA. Therefore, using ctDNA in the clinical setting has the potential to improve therapeutic outcomes. In the present review, we summarize the status of ctDNA in oncology with focus of being an alternative to tissue biopsies in early detection and treatment monitoring.
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Affiliation(s)
- Lise Barlebo Ahlborn
- Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark.,Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
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14
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Ahlborn LB, Rohrberg KS, Gabrielaite M, Tuxen IV, Yde CW, Spanggaard I, Santoni-Rugiu E, Nielsen FC, Lassen U, Mau-Sorensen M, Østrup O. Application of cell-free DNA for genomic tumor profiling: a feasibility study. Oncotarget 2019; 10:1388-1398. [PMID: 30858924 PMCID: PMC6402712 DOI: 10.18632/oncotarget.26642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/17/2019] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Access to genomic tumor material is required to select patients for targeted therapies. However, tissue biopsies are not always feasible and therefore circulating cell-free DNA (cfDNA) has emerged as an alternative. Here we investigate the utility of cfDNA for genomic tumor profiling in the phase I setting. STUDY DESIGN Peripheral blood was collected from patients with advanced solid cancers eligible for phase I treatment. Patients failing the initial tissue biopsy due to inaccessible lesions or insufficient tumor cellularity (<10%) were included in the study. Genomic profiling of cfDNA including whole exome sequencing (WES) and somatic copy number alterations (SCNAs) analysis (OncoScan). RESULTS Plasma cfDNA was pro- and retrospectively profiled from 24 and 20 patients, respectively. The median turnaround time was 29 days (N= 24, range 13-87 days) compared to tissue re-analyses of median 60 days (N= 6, range 29-98). Selected cancer-associated alterations (SCAAs) were identified in 70% (31/44) of patients, predominantly by WES due to the low sensitivity of OncoScan on cfDNA. Primarily, inaccessible cases of prostate and lung cancers could benefit from cfDNA profiling. In contrast, breast cancer patients showed a low level of tumor-specific cfDNA which might be due to cancer type and/or active treatment at the time of plasma collection. CONCLUSION Plasma cfDNA profiling using WES is feasible within a clinically relevant timeframe and represents an alternative to invasive tissue biopsies to identify possible treatment targets. Especially, difficult-to-biopsy cancers can benefit from cfDNA profiling, but tumor tissue remains the gold standard for molecular analyses.
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Affiliation(s)
- Lise B. Ahlborn
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Kristoffer S. Rohrberg
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ida V. Tuxen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Christina W. Yde
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Iben Spanggaard
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
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15
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Mendis S, Loree JM. Clinical application of cfDNA: moving in the right direction, but still a long way to go. Oncotarget 2018; 9:35199-35200. [PMID: 30443285 PMCID: PMC6219669 DOI: 10.18632/oncotarget.26224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 11/29/2022] Open
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