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Bleckman RF, Haag CMSC, Rifaela N, Beukema G, Mathijssen RHJ, Steeghs N, Gelderblom H, Desar IME, Cleven A, Ter Elst A, Schuuring E, Reyners AKL. Levels of circulating tumor DNA correlate with tumor volume in gastro-intestinal stromal tumors: an exploratory long-term follow-up study. Mol Oncol 2024. [PMID: 38790141 DOI: 10.1002/1878-0261.13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 05/26/2024] Open
Abstract
Patients with gastro-intestinal stromal tumors (GISTs) undergoing tyrosine kinase inhibitor therapy are monitored with regular computed tomography (CT) scans, exposing patients to cumulative radiation. This exploratory study aimed to evaluate circulating tumor DNA (ctDNA) testing to monitor treatment response and compare changes in ctDNA levels with RECIST 1.1 and total tumor volume measurements. Between 2014 and 2021, six patients with KIT proto-oncogene, receptor tyrosine kinase (KIT) exon-11-mutated GIST from whom long-term plasma samples were collected prospectively were included in the study. ctDNA levels of relevant plasma samples were determined using the KIT exon 11 digital droplet PCR drop-off assay. Tumor volume measurements were performed using a semi-automated approach. In total, 94 of 130 clinically relevant ctDNA samples were analyzed. Upon successful treatment response, ctDNA became undetectable in all patients. At progressive disease, ctDNA was detectable in five out of six patients. Higher levels of ctDNA correlated with larger tumor volumes. Undetectable ctDNA at the time of progressive disease on imaging was consistent with lower tumor volumes compared to those with detectable ctDNA. In summary, ctDNA levels seem to correlate with total tumor volume at the time of progressive disease. Our exploratory study shows promise for including ctDNA testing in treatment follow-up.
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Affiliation(s)
- Roos F Bleckman
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Charlotte M S C Haag
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Naomi Rifaela
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Gerrieke Beukema
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Ingrid M E Desar
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Cleven
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Arja Ter Elst
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ed Schuuring
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Anna K L Reyners
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
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2
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van der Leest P, Janning M, Rifaela N, Azpurua MLA, Kropidlowski J, Loges S, Lozano N, Sartori A, Irwin D, Lamy PJ, Hiltermann TJN, Groen HJM, Pantel K, van Kempen LC, Wikman H, Schuuring E. Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients. Int J Mol Sci 2023; 24:13390. [PMID: 37686200 PMCID: PMC10487510 DOI: 10.3390/ijms241713390] [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: 07/29/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) is a potential minimally invasive molecular tool to guide treatment decision-making and disease monitoring. A suitable diagnostic-grade platform is required for the detection of tumor-specific mutations with high sensitivity in the circulating cell-free DNA (ccfDNA) of cancer patients. In this multicenter study, the ccfDNA of 72 patients treated for advanced-stage non-small cell lung cancer (NSCLC) was evaluated using the UltraSEEK® Lung Panel on the MassARRAY® System, covering 73 hotspot mutations in EGFR, KRAS, BRAF, ERBB2, and PIK3CA against mutation-specific droplet digital PCR (ddPCR) and routine tumor tissue NGS. Variant detection accuracy at primary diagnosis and during disease progression, and ctDNA dynamics as a marker of treatment efficacy, were analyzed. A multicenter evaluation using reference material demonstrated an overall detection rate of over 90% for variant allele frequencies (VAFs) > 0.5%, irrespective of ccfDNA input. A comparison of UltraSEEK® and ddPCR analyses revealed a 90% concordance. An 80% concordance between therapeutically targetable mutations detected in tumor tissue NGS and ccfDNA UltraSEEK® analysis at baseline was observed. Nine of 84 (11%) tumor tissue mutations were not covered by UltraSEEK®. A decrease in ctDNA levels at 4-6 weeks after treatment initiation detected with UltraSEEK® correlated with prolonged median PFS (46 vs. 6 weeks; p < 0.05) and OS (145 vs. 30 weeks; p < 0.01). Using plasma-derived ccfDNA, the UltraSEEK® Lung Panel with a mid-density set of the most common predictive markers for NSCLC is an alternative tool to detect mutations both at diagnosis and during disease progression and to monitor treatment response.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Melanie Janning
- German Cancer Research Center (DKFZ)-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany;
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Naomi Rifaela
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Maria L. Aguirre Azpurua
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Jolanthe Kropidlowski
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Sonja Loges
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Nicolas Lozano
- Institut d’Analyse Génomique Imagenome, Labosud, 34070 Montpellier, France
| | | | | | - Pierre-Jean Lamy
- Institut d’Analyse Génomique Imagenome, Labosud, 34070 Montpellier, France
- Department of Clinical Research, Clinique BeauSoleil, 34070 Montpellier, France
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.)
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Léon C. van Kempen
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Ed Schuuring
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
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3
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Yu Q, Jiang H, Su X, Jiang Z, Liang X, Zhang C, Shang W, Zhang Y, Chen H, Yang Z, Shen M, Huang F, Chen X, Yang Y, Pan B, Wang B, Lu D, Guo W. Development of multiplex drop-off digital PCR assays for hotspot mutation detection of KRAS, NRAS, BRAF and PIK3CA in the plasma of colorectal cancer patients. J Mol Diagn 2023; 25:388-402. [PMID: 36963484 DOI: 10.1016/j.jmoldx.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The detection of mutations in KRAS, NRAS, BRAF and PIK3CA has become essential in treatment management of metastatic colorectal cancer (mCRC), with the approval of new targeted therapies. We developed novel multiplex drop-off digital PCR (MDO-dPCR) assays, by combining amplitude-/ratio-based multiplexing with drop-off/double drop-off strategies, which allow for detection of at least 69 most frequent hotspot mutations in all four genes with only three reactions. We assessed the analytical performance of the assays using synthetic oligonucleotides, further validated on plasma cfDNA samples from a large cohort of CRC patients and compared with next generation sequencing (NGS) data. The MDO-dPCR assays showed a high sensitivity with a limit of detection (LOD) ranging from 0.084 to 0.182% in mutant allelic frequency (MAF). The screening of plasma cfDNAs from 106 CRC patients identified mutations in 42.45% of them, with a sensitivity of 95.24%, a specificity of 98.53% and an accuracy of 96.98% for mutation detection and a strong correlation of measured MAFs as compared to NGS results. The high sensitivity and comprehensive mutation coverage of the MDO-dPCR assays make them suitable for rapid and cost-effective detection of KRAS, NRAS, BRAF and PIK3CA mutations in the plasma of CRC patients, and could be useful in early response assessment and longitudinal disease monitoring.
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Affiliation(s)
- Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Huiqin Jiang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Su
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Xue Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Wu Shang
- Nanjing Pregene Biotechnology, Nanjing, China
| | | | - Hao Chen
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Zhijie Yang
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinning Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihui Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
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4
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Falkenhorst J, Grunewald S, Krzeciesa D, Herold T, Ketzer J, Christoff M, Hamacher R, Kostbade K, Treckmann J, Köster J, Farzaliyev F, Fletcher BS, Dieckmann N, Kaths M, Mühlenberg T, Schildhaus HU, Bauer S. Plasma Sequencing for Patients with GIST-Limitations and Opportunities in an Academic Setting. Cancers (Basel) 2022; 14:5496. [PMID: 36428589 PMCID: PMC9688348 DOI: 10.3390/cancers14225496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Circulating tumor DNA (ctDNA) from circulating free DNA (cfDNA) in GIST is of interest for the detection of heterogeneous resistance mutations and treatment monitoring. However, methodologies for use in a local setting are not standardized and are error-prone and difficult to interpret. We established a workflow to evaluate routine tumor tissue NGS (Illumina-based next generation sequencing) panels and pipelines for ctDNA sequencing in an academic setting. Regular blood collection (Sarstedt) EDTA tubes were sufficient for direct processing whereas specialized tubes (STRECK) were better for transportation. Mutation detection rate was higher in automatically extracted (AE) than manually extracted (ME) samples. Sensitivity and specificity for specific mutation detection was higher using digital droplet (dd)PCR compared to NGS. In a retrospective analysis of NGS and clinical data (133 samples from 38 patients), cfDNA concentration correlated with tumor load and mutation detection. A clinical routine pipeline and a novel research pipeline yielded different results, but known and resistance-mediating mutations were detected by both and correlated with the resistance spectrum of TKIs used. In conclusion, NGS routine panel analysis was not sensitive and specific enough to replace solid biopsies in GIST. However, more precise methods (hybridization capture NGS, ddPCR) may comprise important research tools to investigate resistance. Future clinical trials need to compare methodology and protocols.
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Affiliation(s)
- Johanna Falkenhorst
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Susanne Grunewald
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Dawid Krzeciesa
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Thomas Herold
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Institute of Pathology, University Medical Center Essen, 45147 Essen, Germany
| | - Julia Ketzer
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Miriam Christoff
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Rainer Hamacher
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Karina Kostbade
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Jürgen Treckmann
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Department of Visceral Surgery, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Johannes Köster
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Farhad Farzaliyev
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Department of Visceral Surgery, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Benjamin Samulon Fletcher
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Nils Dieckmann
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Moritz Kaths
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Department of Visceral Surgery, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Thomas Mühlenberg
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Hans-Ulrich Schildhaus
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
- Institute of Pathology, University Medical Center Essen, 45147 Essen, Germany
| | - Sebastian Bauer
- Department of Medical Oncology, Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
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5
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Ko TK, Lee E, Ng CCY, Yang VS, Farid M, Teh BT, Chan JY, Somasundaram N. Circulating Tumor DNA Mutations in Progressive Gastrointestinal Stromal Tumors Identify Biomarkers of Treatment Resistance and Uncover Potential Therapeutic Strategies. Front Oncol 2022; 12:840843. [PMID: 35273917 PMCID: PMC8904145 DOI: 10.3389/fonc.2022.840843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 12/27/2022] Open
Abstract
Liquid biopsy circulating tumor DNA (ctDNA)-based approaches may represent a non-invasive means for molecular interrogation of gastrointestinal stromal tumors (GISTs). We deployed a customized 29-gene Archer® LiquidPlex™ targeted panel on 64 plasma samples from 46 patients. The majority were known to harbor KIT mutations (n = 41, 89.1%), while 3 were PDGFRA exon 18 D842V mutants and the rest (n = 2) were wild type for KIT and PDGFRA. In terms of disease stage, 14 (30.4%) were localized GISTs that had undergone complete surgical resection while the rest (n = 32) were metastatic. Among ten patients, including 7 on tyrosine kinase inhibitors, with evidence of disease progression at study inclusion, mutations in ctDNA were detected in 7 cases (70%). Known somatic mutations in KIT (n = 5) or PDGFRA (n = 1) in ctDNA were identified only among 6 of the 10 patients. These KIT mutants included duplication, indels, and single-nucleotide variants. The median mutant AF in ctDNA was 11.0% (range, 0.38%–45.0%). In patients with metastatic progressive KIT-mutant GIST, tumor burden was higher with detectable KIT ctDNA mutation than in those without (median, 5.97 cm vs. 2.40 cm, p = 0.0195). None of the known tumor mutations were detected in ctDNA for localized cases (n = 14) or metastatic cases without evidence of disease progression (n = 22). In patients with serial samples along progression of disease, secondary acquired mutations, including a potentially actionable PIK3CA exon 9 c.1633G>A mutation, were detected. ctDNA mutations were not detectable when patients responded to a switch in TKI therapy. In conclusion, detection of GIST-related mutations in ctDNA using a customized targeted NGS panel represents an attractive non-invasive means to obtain clinically tractable information at the time of disease progression.
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Affiliation(s)
- Tun Kiat Ko
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.,Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Elizabeth Lee
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.,Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Cedric Chuan-Young Ng
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.,Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Valerie Shiwen Yang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.,Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nagavalli Somasundaram
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
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7
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Johansson G, Berndsen M, Lindskog S, Österlund T, Fagman H, Muth A, Ståhlberg A. Monitoring Circulating Tumor DNA During Surgical Treatment in Patients with Gastrointestinal Stromal Tumors. Mol Cancer Ther 2021; 20:2568-2576. [PMID: 34552011 PMCID: PMC9398151 DOI: 10.1158/1535-7163.mct-21-0403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 09/14/2021] [Indexed: 01/07/2023]
Abstract
The majority of patients diagnosed with advanced gastrointestinal stromal tumors (GISTs) are successfully treated with a combination of surgery and tyrosine kinase inhibitors (TKIs). However, it remains challenging to monitor treatment efficacy and identify relapse early. Here, we utilized a sequencing strategy based on molecular barcodes and developed a GIST-specific panel to monitor tumor-specific and TKI resistance mutations in cell-free DNA and applied the approach to patients undergoing surgical treatment. Thirty-two patients with GISTs were included, and 161 blood plasma samples were collected and analyzed at routine visits before and after surgery and at the beginning, during, and after surgery. Patients were included regardless of their risk category. Our GIST-specific sequencing approach allowed detection of tumor-specific mutations and TKI resistance mutations with mutant allele frequency < 0.1%. Circulating tumor DNA (ctDNA) was detected in at least one timepoint in nine of 32 patients, ranging from 0.04% to 93% in mutant allele frequency. High-risk patients were more often ctDNA positive than other risk groups (P < 0.05). Patients with detectable ctDNA also displayed higher tumor cell proliferation rates (P < 0.01) and larger tumor sizes (P < 0.01). All patients who were ctDNA positive during surgery became negative after surgery. Finally, in two patients who progressed on TKI treatment, we detected multiple resistance mutations. Our data show that ctDNA may become a clinically useful biomarker in monitoring treatment efficacy in patients with high-risk GISTs and can assist in treatment decision making.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marta Berndsen
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Stefan Lindskog
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Surgery, Halland Regional Hospital Varberg, Region Halland, Varberg, Sweden
| | - Tobias Österlund
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henrik Fagman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Andreas Muth
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Section of Endocrine and Sarcoma Surgery, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Corresponding Authors: Anders Ståhlberg, Sahlgrenska Center for Cancer Research, University of Gothenburg, Box 425, Gothenburg 405 30, Sweden. E-mail: ; and Andreas Muth, Department of Surgery, Sahlgrenska University Hospital, Blå stråket 5, 413 45 Gothenburg, Sweden. E-mail:
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Corresponding Authors: Anders Ståhlberg, Sahlgrenska Center for Cancer Research, University of Gothenburg, Box 425, Gothenburg 405 30, Sweden. E-mail: ; and Andreas Muth, Department of Surgery, Sahlgrenska University Hospital, Blå stråket 5, 413 45 Gothenburg, Sweden. E-mail:
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8
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van der Leest P, Hiddinga B, Miedema A, Aguirre Azpurua ML, Rifaela N, ter Elst A, Timens W, Groen HJM, van Kempen LC, Hiltermann TJN, Schuuring E. Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors. Mol Oncol 2021; 15:2910-2922. [PMID: 34449963 PMCID: PMC8564646 DOI: 10.1002/1878-0261.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/07/2022] Open
Abstract
Immunotherapy for metastasized non-small-cell lung cancer (NSCLC) can show long-lasting clinical responses. Selection of patients based on programmed death-ligand 1 (PD-L1) expression shows limited predictive value for durable clinical benefit (DCB). We investigated whether early treatment effects as measured by a change in circulating tumor DNA (ctDNA) level is a proxy of early tumor response to immunotherapy according to response evaluation criteria in solid tumors v1.1 criteria, progression-free survival (PFS), DCB, and overall survival (OS). To this aim, blood tubes were collected from advanced-stage lung adenocarcinoma patients (n = 100) receiving immune checkpoint inhibitors (ICI) at baseline (t0 ) and prior to first treatment evaluation (4-6 weeks; t1 ). Nontargetable (driver) mutations detected in the pretreatment tumor biopsy were used to quantify tumor-specific ctDNA levels using droplet digital PCR. We found that changes in ctDNA levels were strongly associated with tumor response. A > 30% decrease in ctDNA at t1 correlated with a longer PFS and OS. In total, 80% of patients with a DCB of ≥ 26 weeks displayed a > 30% decrease in ctDNA levels. For patients with a PD-L1 tumor proportion score of ≥ 1%, decreasing ctDNA levels were associated with a higher frequency a DCB (80%) and a prolonged median PFS (85 weeks) and OS (101 weeks) compared with patients with no decrease in ctDNA (34%; 11 and 39 weeks, respectively). This study shows that monitoring of ctDNA dynamics is an easy-to-use and promising tool for assessing PFS, DCB, and OS for ICI-treated NSCLC patients.
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Affiliation(s)
- Paul van der Leest
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Birgitta Hiddinga
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Anneke Miedema
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Maria L. Aguirre Azpurua
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Naomi Rifaela
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Arja ter Elst
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Wim Timens
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Harry J. M. Groen
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Léon C. van Kempen
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Ed Schuuring
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
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9
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van der Laan P, van Houdt WJ, van den Broek D, Steeghs N, van der Graaf WTA. Liquid Biopsies in Sarcoma Clinical Practice: Where Do We Stand? Biomedicines 2021; 9:1315. [PMID: 34680432 PMCID: PMC8533081 DOI: 10.3390/biomedicines9101315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Sarcomas are rare tumors of bone and soft tissue with a mesenchymal origin. This uncommon type of cancer is marked by a high heterogeneity, consisting of over 70 subtypes. Because of this broad spectrum, their treatment requires a subtype-specific therapeutic approach. Tissue biopsy is currently the golden standard for sarcoma diagnosis, but it has its limitations. Over the recent years, methods to detect, characterize, and monitor cancer through liquid biopsy have evolved rapidly. The analysis of circulating biomarkers in peripheral blood, such as circulating tumor cells (CTC) or circulating tumor DNA (ctDNA), could provide real-time information on tumor genetics, disease state, and resistance mechanisms. Furthermore, it traces tumor evolution and can assess tumor heterogeneity. Although the first results in sarcomas are encouraging, there are technical challenges that need to be addressed for implementation in clinical practice. Here, we summarize current knowledge about liquid biopsies in sarcomas and elaborate on different strategies to integrate liquid biopsy into sarcoma clinical care.
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Affiliation(s)
- Pia van der Laan
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winette T. A. van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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10
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Koopman B, Cajiao Garcia BN, Kuijpers CCHJ, Damhuis RAM, van der Wekken AJ, Groen HJM, Schuuring E, Willems SM, van Kempen LC. A Nationwide Study on the Impact of Routine Testing for EGFR Mutations in Advanced NSCLC Reveals Distinct Survival Patterns Based on EGFR Mutation Subclasses. Cancers (Basel) 2021; 13:3641. [PMID: 34298851 PMCID: PMC8307492 DOI: 10.3390/cancers13143641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
EGFR mutation analysis in non-small-cell lung cancer (NSCLC) patients is currently standard-of-care. We determined the uptake of EGFR testing, test results and survival of EGFR-mutant NSCLC patients in the Netherlands, with the overall objective to characterize the landscape of clinically actionable EGFR mutations and determine the role and clinical relevance of uncommon and composite EGFR mutations. Non-squamous NSCLC patients diagnosed in 2013, 2015 and 2017 were identified in the Netherlands Cancer Registry (NCR) and matched to the Dutch Pathology Registry (PALGA). Overall, 10,254 patients were included. Between 2013-2017, the uptake of EGFR testing gradually increased from 72.7% to 80.9% (p < 0.001). Multi-gene testing via next-generation sequencing (increased from 7.8% to 78.7% (p < 0.001), but did not affect the number of detected EGFR mutations (n = 925; 11.7%; 95% confidence interval (CI), 11.0-12.4) nor the distribution of variants. For patients treated with first-line EGFR inhibitors (n = 651), exon 19 deletions were associated with longer OS than L858R (HR 1.58; 95% CI, 1.30-1.92; p < 0.001) or uncommon, actionable variants (HR 2.13; 95% CI, 1.60-2.84; p < 0.001). Interestingly, OS for patients with L858R was similar to those with uncommon, actionable variants (HR 1.31; 95% CI, 0.98-1.75; p = 0.069). Our analysis indicates that grouping exon 19 deletions and L858R into one class of 'common' EGFR mutations in a clinical trial may mask the true activity of an EGFR inhibitor towards specific mutations.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Betzabel N. Cajiao Garcia
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | | | - Ronald A. M. Damhuis
- Netherlands Comprehensive Cancer Organisation (IKNL), P.O. Box 19079, 3501 DB Utrecht, The Netherlands;
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (A.J.v.d.W.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (A.J.v.d.W.); (H.J.M.G.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
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11
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Rausch C, Rothenberg-Thurley M, Buerger SA, Tschuri S, Dufour A, Neusser M, Schneider S, Spiekermann K, Metzeler KH, Ziemann F. Double Drop-Off Droplet Digital PCR: A Novel, Versatile Tool for Mutation Screening and Residual Disease Monitoring in Acute Myeloid Leukemia Using Cellular or Cell-Free DNA. J Mol Diagn 2021; 23:975-985. [PMID: 34020042 DOI: 10.1016/j.jmoldx.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
In acute myeloid leukemia (AML), somatic gene mutations are important prognostic markers and increasingly constitute therapeutic targets. Therefore, robust, sensitive, and fast diagnostic assays are needed. Current techniques for mutation screening and quantification, including next-generation sequencing and quantitative PCR, each have weaknesses that leave a need for novel diagnostic tools. We established double drop-off digital droplet PCR (DDO-ddPCR) assays for gene mutations in NPM1, IDH2, and NRAS, which can detect and quantify diverse alterations at two nearby hotspot regions present in these genes. These assays can be used for mutation screening as well as quantification and sequential monitoring. The assays were validated against next-generation sequencing and existing ddPCR assays and achieved high concordance with an overall sensitivity comparable to conventional digital PCR. In addition, the feasibility of detecting and monitoring genetic alterations in peripheral blood cell-free DNA (cfDNA) of patients with AML by DDO-ddPCR was studied. cfDNA analysis was found to have similar sensitivity compared to quantitative PCR-based analysis of peripheral blood. Finally, the cfDNA-based digital PCR in several clinical scenarios was found to be useful in long-term monitoring of target-specific therapy, early response assessment during induction chemotherapy, and identification of mutations in patients with extramedullary disease. Thus, DDO-ddPCR-based cfDNA analysis may complement existing genetic tools for diagnosis and disease monitoring in AML.
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Affiliation(s)
- Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Simon A Buerger
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Annika Dufour
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Michaela Neusser
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Institute of Human Genetics, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Klaus H Metzeler
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany; Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, Leipzig, Germany.
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Hematology and Oncology, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
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12
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Gómez-Peregrina D, García-Valverde A, Pilco-Janeta D, Serrano C. Liquid Biopsy in Gastrointestinal Stromal Tumors: Ready for Prime Time? Curr Treat Options Oncol 2021; 22:32. [PMID: 33641024 DOI: 10.1007/s11864-021-00832-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
OPINION STATEMENT Gastrointestinal stromal tumor (GIST) constitutes a paradigm for clinically effective targeted inhibition of oncogenic driver mutations. Therefore, GIST has emerged as a compelling clinical and biological model to study oncogene addiction and to validate preclinical concepts for drug response and drug resistance. Oncogenic activation of KIT or PDGFRA receptor tyrosine kinases is the essential drivers of GIST progression throughout all stages of the disease. Interestingly, KIT/PDGFRA genotype predicts the response to first-line imatinib and to all tyrosine kinase inhibitors (TKIs) approved or in investigation after imatinib failure. Considering that TKIs are effective only against a subset of KIT or PDGFRA resistance mutations, close monitoring of tumor dynamics with non-invasive methods such as liquid biopsy emerges as a necessary step forward in the field. Liquid biopsy, in contrast to solid tumor biopsy, aims to characterize tumors irrespective of heterogeneity. Although there are several components in the peripheral blood, most recent studies have been focused on circulating tumor (ct)DNA, due to the technological feasibility, the stability of DNA itself and DNA alterations, and the therapeutic development in precision oncology largely based on the identification of genetic driver mutations. In the present review, we systematically dissect the current wealth of data of ctDNA in GIST. To do so, a critical understanding of the promises and limitations of the current technologies will be followed by an exposition of the knowledge gathered with such studies in GIST. Collectively, our goal is to establish clear premises that can be used as the foundations to build future studies towards the clinical implementation of ctDNA evaluation in GIST patients.
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Affiliation(s)
- David Gómez-Peregrina
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - Alfonso García-Valverde
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - Daniel Pilco-Janeta
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain
| | - César Serrano
- Sarcoma Translational Research Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital Campus, C/ Natzaret 115-117, 08035, Barcelona, Spain. .,Department of Medical Oncology, Vall d'Hebron University Hospital, P/Vall d'Hebron 119, 08035, Barcelona, Spain.
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13
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Grünewald TGP, Alonso M, Avnet S, Banito A, Burdach S, Cidre‐Aranaz F, Di Pompo G, Distel M, Dorado‐Garcia H, Garcia‐Castro J, González‐González L, Grigoriadis AE, Kasan M, Koelsche C, Krumbholz M, Lecanda F, Lemma S, Longo DL, Madrigal‐Esquivel C, Morales‐Molina Á, Musa J, Ohmura S, Ory B, Pereira‐Silva M, Perut F, Rodriguez R, Seeling C, Al Shaaili N, Shaabani S, Shiavone K, Sinha S, Tomazou EM, Trautmann M, Vela M, Versleijen‐Jonkers YMH, Visgauss J, Zalacain M, Schober SJ, Lissat A, English WR, Baldini N, Heymann D. Sarcoma treatment in the era of molecular medicine. EMBO Mol Med 2020; 12:e11131. [PMID: 33047515 PMCID: PMC7645378 DOI: 10.15252/emmm.201911131] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Sarcomas are heterogeneous and clinically challenging soft tissue and bone cancers. Although constituting only 1% of all human malignancies, sarcomas represent the second most common type of solid tumors in children and adolescents and comprise an important group of secondary malignancies. More than 100 histological subtypes have been characterized to date, and many more are being discovered due to molecular profiling. Owing to their mostly aggressive biological behavior, relative rarity, and occurrence at virtually every anatomical site, many sarcoma subtypes are in particular difficult-to-treat categories. Current multimodal treatment concepts combine surgery, polychemotherapy (with/without local hyperthermia), irradiation, immunotherapy, and/or targeted therapeutics. Recent scientific advancements have enabled a more precise molecular characterization of sarcoma subtypes and revealed novel therapeutic targets and prognostic/predictive biomarkers. This review aims at providing a comprehensive overview of the latest advances in the molecular biology of sarcomas and their effects on clinical oncology; it is meant for a broad readership ranging from novices to experts in the field of sarcoma.
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Affiliation(s)
- Thomas GP Grünewald
- Max‐Eder Research Group for Pediatric Sarcoma BiologyInstitute of PathologyFaculty of MedicineLMU MunichMunichGermany
- Division of Translational Pediatric Sarcoma ResearchGerman Cancer Research Center (DKFZ), Hopp Children's Cancer Center (KiTZ), German Cancer Consortium (DKTK)HeidelbergGermany
- Institute of PathologyHeidelberg University HospitalHeidelbergGermany
| | - Marta Alonso
- Program in Solid Tumors and BiomarkersFoundation for the Applied Medical ResearchUniversity of Navarra PamplonaPamplonaSpain
| | - Sofia Avnet
- Orthopedic Pathophysiology and Regenerative Medicine UnitIRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Ana Banito
- Pediatric Soft Tissue Sarcoma Research GroupGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Stefan Burdach
- Department of Pediatrics and Children's Cancer Research Center (CCRC)Technische Universität MünchenMunichGermany
| | - Florencia Cidre‐Aranaz
- Max‐Eder Research Group for Pediatric Sarcoma BiologyInstitute of PathologyFaculty of MedicineLMU MunichMunichGermany
| | - Gemma Di Pompo
- Orthopedic Pathophysiology and Regenerative Medicine UnitIRCCS Istituto Ortopedico RizzoliBolognaItaly
| | | | | | | | | | | | - Merve Kasan
- Max‐Eder Research Group for Pediatric Sarcoma BiologyInstitute of PathologyFaculty of MedicineLMU MunichMunichGermany
| | | | | | - Fernando Lecanda
- Division of OncologyAdhesion and Metastasis LaboratoryCenter for Applied Medical ResearchUniversity of NavarraPamplonaSpain
| | - Silvia Lemma
- Orthopedic Pathophysiology and Regenerative Medicine UnitIRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Dario L Longo
- Institute of Biostructures and Bioimaging (IBB)Italian National Research Council (CNR)TurinItaly
| | | | | | - Julian Musa
- Max‐Eder Research Group for Pediatric Sarcoma BiologyInstitute of PathologyFaculty of MedicineLMU MunichMunichGermany
- Department of General, Visceral and Transplantation SurgeryUniversity of HeidelbergHeidelbergGermany
| | - Shunya Ohmura
- Max‐Eder Research Group for Pediatric Sarcoma BiologyInstitute of PathologyFaculty of MedicineLMU MunichMunichGermany
| | | | - Miguel Pereira‐Silva
- Department of Pharmaceutical TechnologyFaculty of PharmacyUniversity of CoimbraCoimbraPortugal
| | - Francesca Perut
- Orthopedic Pathophysiology and Regenerative Medicine UnitIRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Rene Rodriguez
- Instituto de Investigación Sanitaria del Principado de AsturiasOviedoSpain
- CIBER en oncología (CIBERONC)MadridSpain
| | | | - Nada Al Shaaili
- Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Shabnam Shaabani
- Department of Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Kristina Shiavone
- Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Snehadri Sinha
- Department of Oral and Maxillofacial DiseasesUniversity of HelsinkiHelsinkiFinland
| | | | - Marcel Trautmann
- Division of Translational PathologyGerhard‐Domagk‐Institute of PathologyMünster University HospitalMünsterGermany
| | - Maria Vela
- Hospital La Paz Institute for Health Research (IdiPAZ)MadridSpain
| | | | | | - Marta Zalacain
- Institute of Biostructures and Bioimaging (IBB)Italian National Research Council (CNR)TurinItaly
| | - Sebastian J Schober
- Department of Pediatrics and Children's Cancer Research Center (CCRC)Technische Universität MünchenMunichGermany
| | - Andrej Lissat
- University Children′s Hospital Zurich – Eleonoren FoundationKanton ZürichZürichSwitzerland
| | - William R English
- Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Nicola Baldini
- Orthopedic Pathophysiology and Regenerative Medicine UnitIRCCS Istituto Ortopedico RizzoliBolognaItaly
- Department of Biomedical and Neuromotor SciencesUniversity of BolognaBolognaItaly
| | - Dominique Heymann
- Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
- Université de NantesInstitut de Cancérologie de l'OuestTumor Heterogeneity and Precision MedicineSaint‐HerblainFrance
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14
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Arshad J, Roberts A, Ahmed J, Cotta J, Pico BA, Kwon D, Trent JC. Utility of Circulating Tumor DNA in the Management of Patients With GI Stromal Tumor: Analysis of 243 Patients. JCO Precis Oncol 2020; 4:66-73. [DOI: 10.1200/po.19.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE GI stromal tumor (GIST) is the most common sarcoma of the GI tract. Management of patients with GIST is determined by KIT, PDGFRA, or other genomic alterations. Tissue-based next-generation sequencing (NGS) analysis is the standard approach for diagnosis, prognosis, and treatment selection. However, circulating tumor DNA (ctDNA)–based NGS is a novel and noninvasive alternative. METHODS ctDNA sequencing results were evaluated in blood samples from 243 de-identified patients within the Guardant360 database. Under an approved institutional review board protocol, a retrospective analysis was performed on 45 single-institution patients. RESULTS Of 243 patients, 114 (47%) were women, and the median age was 59 years (range, 17-90 years). Patients with no alterations and variations of uncertain significance were excluded. Of the 162 patients with known pathogenic mutations, KIT was the most common (56%), followed by NF (7%), PDGFRA (6%), PI3KCA (6%), KRAS (5%), and others (6%). Most tumors harbored an actionable KIT or PDGFRA mutation. Our institutional cohort (n = 45) had 16 (35%) KIT exon 11 mutations, 3 (6%) KIT exon 9 mutations, and 1 (2%) PDGFRA mutation detected on ctDNA. Resistance mutations were observed in KIT exon 17 (8 patients), exon 13 (3 patients), and in both (3 patients). Our comparison of ctDNA with tissue NGS revealed a positive predictive value (PPV) of 100%. Failure of concordance was observed in patients with localized or low disease burden. From the time of ctDNA testing, the median overall survival was not reached, whereas the median progression-free survival was 7 months. CONCLUSION ctDNA provides a rapid, noninvasive analysis of current mutations with a high PPV for patients with metastatic GIST. ctDNA-based testing may help to define the optimal choice of therapy on the basis of resistance mutations and should be studied prospectively.
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Affiliation(s)
- Junaid Arshad
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | | | | | - Jared Cotta
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Brian A. Pico
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Deukoo Kwon
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
| | - Jonathan C. Trent
- University of Miami, Miller School of Medicine/Sylvester Comprehensive Cancer Center, Miami, FL
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15
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Wang Y, Call J. Mutational Testing in Gastrointestinal Stromal Tumor. Curr Cancer Drug Targets 2020; 19:688-697. [PMID: 30914028 DOI: 10.2174/1568009619666190326123945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/05/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022]
Abstract
Targeted treatment has become a major modality in cancer management. Such cancer drugs are generally designed to treat tumors with certain genetic/genomic makeups. Mutational testing prior to prescribing targeted therapy is crucial in identifying who can receive clinical benefit from specific cancer drugs. Over the last two decades, gastrointestinal stromal tumors (GISTs) have evolved from histogenetically obscure to being identified as distinct gastrointestinal mesenchymal tumors with well-defined clinical and molecular characteristics, for which multiple lines of targeted therapies are available. Although the National Comprehensive Cancer Network (NCCN) strongly recommends mutational testing for optimal management of GIST, many GIST patients still have neither a mutation test performed or any mutation-guided cancer management. Here, we review the mutation-guided landscape of GIST, mutational testing methods, and the recent development of new therapies targeting GIST with specific mutations.
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Affiliation(s)
- Yu Wang
- The Life Raft Group, 155 US-46 Wayne, NJ 07470, United States
| | - Jerry Call
- The Life Raft Group, 155 US-46 Wayne, NJ 07470, United States
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16
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Wei J, Liu X, Li T, Xing P, Zhang C, Yang J. The new horizon of liquid biopsy in sarcoma: the potential utility of circulating tumor nucleic acids. J Cancer 2020; 11:5293-5308. [PMID: 32742476 PMCID: PMC7391194 DOI: 10.7150/jca.42816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
The diagnosis, treatment and prognosis of sarcoma are mainly dependent on tissue biopsy, which is limited in its ability to provide a panoramic view into the dynamics of tumor progression. In addition, effective biomarkers to monitor the progression and therapeutic response of sarcoma are lacking. Liquid biopsy, a recent technological breakthrough, has gained great attention in the last few decades. Nucleic acids (such as DNA, mRNAs, microRNAs, and long non-coding RNAs) that are released from tumors circulate in the blood of cancer patients and can be evaluated through liquid biopsy. Circulating tumor nucleic acids reflect the intertumoral and intratumoral heterogeneity, and thus liquid biopsy provides a noninvasive strategy to examine these molecules compared with traditional tissue biopsy. Over the past decade, a great deal of information on the potential utilization of circulating tumor nucleic acids in sarcoma screening, prognosis and therapy efficacy monitoring has emerged. Several specific gene mutations in sarcoma can be detected in peripheral blood samples from patients and can be found in circulating tumor DNA to monitor sarcoma. In addition, circulating tumor non-coding RNA may also be a promising biomarker in sarcoma. In this review, we discuss the clinical application of circulating tumor nucleic acids as blood-borne biomarkers in sarcoma.
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Affiliation(s)
- Junqiang Wei
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde, Hebei, 067000, China
| | - Xinyue Liu
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Ting Li
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Peipei Xing
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Chao Zhang
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Jilong Yang
- Department of bone and soft tissue tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin's Medical University Cancer Institute and Hospital, Tianjin, 300060, China
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17
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van der Leest P, Boonstra PA, ter Elst A, van Kempen LC, Tibbesma M, Koopmans J, Miedema A, Tamminga M, Groen HJM, Reyners AKL, Schuuring E. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers (Basel) 2020; 12:E1222. [PMID: 32414097 PMCID: PMC7281769 DOI: 10.3390/cancers12051222] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) may contain DNA originating from the tumor in plasma of cancer patients (ctDNA) and enables noninvasive cancer diagnosis, treatment predictive testing, and response monitoring. A recent multicenter evaluation of workflows by the CANCER-ID consortium using artificial spiked-in plasma showed significant differences and consequently the importance of carefully selecting ccfDNA extraction methods. Here, the quantity and integrity of extracted ccfDNA from the plasma of cancer patients were assessed. Twenty-one cancer patient-derived cell-free plasma samples were selected to compare the Qiagen CNA, Maxwell RSC ccfDNA plasma, and Zymo manual quick ccfDNA kit. High-volume citrate plasma samples collected by diagnostic leukapheresis from six cancer patients were used to compare the Qiagen CNA (2 mL) and QIAamp MinElute ccfDNA kit (8 mL). This study revealed similar integrity and similar levels of amplified short-sized fragments and tumor-specific mutants comparing the CNA and RSC kits. However, the CNA kit consistently showed the highest yield of ccfDNA and short-sized fragments, while the RSC and ME kits showed higher variant allelic frequencies (VAFs). Our study pinpoints the importance of standardizing preanalytical conditions as well as consensus on defining the input of ccfDNA to accurately detect ctDNA and be able to compare results in a clinical routine practice, within and between clinical studies.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Pieter A. Boonstra
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Marco Tibbesma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Jill Koopmans
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Anneke Miedema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Anna K. L. Reyners
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
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18
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Arshad J, Ahmed J, Subhawong T, Trent JC. Progress in determining response to treatment in gastrointestinal stromal tumor. Expert Rev Anticancer Ther 2020; 20:279-288. [PMID: 32191549 DOI: 10.1080/14737140.2020.1745068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Gastrointestinal stromal tumor (GIST) is the most common malignant mesenchymal tumor of the gastrointestinal system. Multiple advances in the management of GIST from the discovery of KIT/PDGRA and other genetic alterations have led to the development of multiple tyrosine kinase inhibitors. Response assessment in GIST is determined with iRECIST (Response Evaluation Criteria in Solid Tumors), PERCIST (PET response criteria in solid tumors), or Choi criteria. Molecular genotyping of the tissue samples is the recent standard for diagnosis, treatment, and response to treatment.Areas covered: In this study, we provide a brief overview of the history of the GIST, molecular sequencing, available treatment options and clinical trials, radiologic response assessment, and the role of ctDNA in response evaluation.Expert opinion: Future GIST management is related to the development of sensitive assays to detect genetic alterations for initial diagnosis, treatment selection, monitoring the response to treatment, resistant mutations, and predicting survival.
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Affiliation(s)
- Junaid Arshad
- Miller School of Medicine/Sylvester Comprehensive Cancer Centre, University of Miami, Miami, FL, USA
| | - Jibran Ahmed
- Department of Hematology and Medical Oncology, Westchester Medical Center, Valhalla, NY, USA
| | - Ty Subhawong
- Miller School of Medicine/Sylvester Comprehensive Cancer Centre, University of Miami, Miami, FL, USA
| | - Jonathan C Trent
- Miller School of Medicine/Sylvester Comprehensive Cancer Centre, University of Miami, Miami, FL, USA
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19
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Serrano C, Vivancos A, López-Pousa A, Matito J, Mancuso FM, Valverde C, Quiroga S, Landolfi S, Castro S, Dopazo C, Sebio A, Virgili AC, Menso MM, Martín-Broto J, Sansó M, García-Valverde A, Rosell J, Fletcher JA, George S, Carles J, Arribas J. Clinical value of next generation sequencing of plasma cell-free DNA in gastrointestinal stromal tumors. BMC Cancer 2020; 20:99. [PMID: 32024476 PMCID: PMC7003348 DOI: 10.1186/s12885-020-6597-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Gastrointestinal stromal tumor (GIST) initiation and evolution is commonly framed by KIT/PDGFRA oncogenic activation, and in later stages by the polyclonal expansion of resistant subpopulations harboring KIT secondary mutations after the onset of imatinib resistance. Thus, circulating tumor (ct)DNA determination is expected to be an informative non-invasive dynamic biomarker in GIST patients. Methods We performed amplicon-based next-generation sequencing (NGS) across 60 clinically relevant genes in 37 plasma samples from 18 GIST patients collected prospectively. ctDNA alterations were compared with NGS of matched tumor tissue samples (obtained either simultaneously or at the time of diagnosis) and cross-validated with droplet digital PCR (ddPCR). Results We were able to identify cfDNA mutations in five out of 18 patients had detectable in at least one timepoint. Overall, NGS sensitivity for detection of cell-free (cf)DNA mutations in plasma was 28.6%, showing high concordance with ddPCR confirmation. We found that GIST had relatively low ctDNA shedding, and mutations were at low allele frequencies. ctDNA was detected only in GIST patients with advanced disease after imatinib failure, predicting tumor dynamics in serial monitoring. KIT secondary mutations were the only mechanism of resistance found across 10 imatinib-resistant GIST patients progressing to sunitinib or regorafenib. Conclusions ctDNA evaluation with amplicon-based NGS detects KIT primary and secondary mutations in metastatic GIST patients, particularly after imatinib progression. GIST exhibits low ctDNA shedding, but ctDNA monitoring, when positive, reflects tumor dynamics.
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Affiliation(s)
- César Serrano
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain. .,Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain.
| | - Ana Vivancos
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain.
| | | | - Judit Matito
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | - Claudia Valverde
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Sergi Quiroga
- Radiology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Stefania Landolfi
- Pathology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Sandra Castro
- Surgical Oncology Division, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Cristina Dopazo
- Surgical Oncology Division, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ana Sebio
- Medical Oncology, Sant Pau University Hospital, Barcelona, Spain
| | - Anna C Virgili
- Medical Oncology, Sant Pau University Hospital, Barcelona, Spain
| | - María M Menso
- Radiology Department, Sant Pau University Hospital, Barcelona, Spain
| | | | - Miriam Sansó
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | | | - Jordi Rosell
- Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jonathan A Fletcher
- Pathology Department, Brigham and Women's Hospital/Harvard Medical School, Boston, USA
| | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Joan Carles
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Joaquín Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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20
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Tamminga M, de Wit S, Schuuring E, Timens W, Terstappen LWMM, Hiltermann TJN, Groen HJM. Circulating tumor cells in lung cancer are prognostic and predictive for worse tumor response in both targeted- and chemotherapy. Transl Lung Cancer Res 2019; 8:854-861. [PMID: 32010564 DOI: 10.21037/tlcr.2019.11.06] [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] [Indexed: 12/20/2022]
Abstract
Background It is unknown whether the presence of circulating tumor cells (CTC), a known prognostic factor, influences treatment outcome. We investigated whether baseline CTC in non-small cell lung cancer (NSCLC) patients treated with tyrosine kinase inhibitors (TKI) or chemotherapy was associated with response to therapy. Methods We included consecutive advanced NSCLC patients, stratified by therapy. Before treatment the number of CTC was measured by CellSearch. Tumor response rates, progression free survival (PFS) and overall survival (OS) in patients with and without CTC at baseline were compared. Results We included 86 patients (34 treated by TKI). Response rates of patients with CTC were lower than in patients without CTC (OR =0.22, P<0.01, adjusted for performance score and smoking status). In both treatment groups, the difference in response rates between patients with and without CTC was similar (TKI response: 25% with CTC versus 73% without CTC, chemotherapy response: 35% versus 51% respectively, interaction P=0.17). CTC was associated with a worse PFS [hazard ratio (HR) =2.0, 95% confidence interval (CI): 1.2-3.2, P=0.01] and OS (HR =1.7, 95% CI: 1.1-2.8, P=0.03) after adjustment for performance score and stage. The association remained significant after adding tumor response to the model (PFS: HR =1.9, 95% CI: 1.0-3.0, P=0.01, OS: HR =1.6, 95% CI: 1.0-2.6, P=0.05). No significant interaction between CTC presence and therapy was observed (P=0.42 for PFS and P=0.83 for OS). Conclusions Presence of CTC in advanced NSCLC patients is associated with low response rates, shorter PFS and OS, independent of the received therapy.
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Affiliation(s)
- Menno Tamminga
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sanne de Wit
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Leon W M M Terstappen
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, The Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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21
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Tamminga M, de Wit S, Hiltermann TJN, Timens W, Schuuring E, Terstappen LWMM, Groen HJM. Circulating tumor cells in advanced non-small cell lung cancer patients are associated with worse tumor response to checkpoint inhibitors. J Immunother Cancer 2019; 7:173. [PMID: 31291995 PMCID: PMC6617698 DOI: 10.1186/s40425-019-0649-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/21/2019] [Indexed: 12/27/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) patients treated with checkpoint inhibitors show long lasting responses, but it is hard to predict which patients will profit from this treatment with the currently used marker, programmed death ligand 1 (PD-L1). We hypothesized that circulating tumor cells (CTC) or tumor derived extracellular vesicles (tdEV) are markers of treatment efficacy. Methods Patients with advanced NSCLC treated with checkpoint inhibitors were included. Blood was drawn at baseline (T0) and at 4 weeks of treatment (T1) for analysis of CTC and tdEV using CellSearch®. Tumor response was classified as partial or complete response based on the response evaluation criteria in solid tumors (RECISTv1.1) measured 4–6 weeks after start of treatment. Durable response was defined as stable disease, partial or complete response without disease progression at 6 months. Analyses were adjusted for covariables including PD-L1 expression. Results We included 104 patients (30 with a tumor response, 74 non-responders, 2 responses not evaluable due to early death); 63 patients provided T1 samples. All patients were treated with PD-L1 inhibitors. The majority of patients received second (85%) or third line (treatment with nivolumab monotherapy (89%). CTC were present in 33/104 patients at T0 (32%) and 17/63 at T1 (27%), 9/63 patients had CTC (14%) at both time points. The presence of CTC, both at T0 (OR = 0.28, p = 0.02,) and T1 (OR = 0.07, p < 0.01), was an independent predictive factor for a lack of durable response and was associated with worse progression free and overall survival. More tdEV were associated with shorter survival but not with response rate. Conclusion CTC occur in one third of advanced NSCLC patients and their presence is a predictive factor for a worse durable response rate to checkpoint inhibitors. tdEV are associated with shorter survival but not with response. Electronic supplementary material The online version of this article (10.1186/s40425-019-0649-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30.0001, 9700, RB, Groningen, The Netherlands.
| | - Sanne de Wit
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, The Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30.0001, 9700, RB, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Leon W M M Terstappen
- Department of Medical Cell BioPhysics, Faculty of Sciences and Technology, University of Twente, Enschede, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30.0001, 9700, RB, Groningen, The Netherlands
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22
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Jilg S, Rassner M, Maier J, Waldeck S, Kehl V, Follo M, Philipp U, Sauter A, Specht K, Mitschke J, Lange T, Bauer S, Jost PJ, Peschel C, Duyster J, Gaiser T, Hohenberger P, Bubnoff N. Circulating
cKIT
and
PDGFRA
DNA indicates disease activity in Gastrointestinal Stromal Tumor (GIST). Int J Cancer 2019; 145:2292-2303. [DOI: 10.1002/ijc.32282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/10/2019] [Accepted: 03/05/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Stefanie Jilg
- III Medical Department for Hematology and Oncology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Michael Rassner
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
| | - Jacqueline Maier
- Center for Internal Medicine, Department of Hematology/Oncology and HemostaseologyUniversity of Leipzig Leipzig Germany
| | - Silvia Waldeck
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ) Heidelberg Germany
- Faculty of BiologyUniversity of Freiburg Freiburg Germany
| | - Victoria Kehl
- Institute for Medical Informatics, Statistics, and Epidemiology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Marie Follo
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
| | - Ulrike Philipp
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
| | - Andreas Sauter
- Department of Diagnostic and Interventional Radiology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Katja Specht
- Institute of Pathology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Jan Mitschke
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ) Heidelberg Germany
| | | | - Sebastian Bauer
- Sarcoma Center, West German Cancer CenterUniversity Hospital Essen, University Duisburg‐Essen Essen Germany
| | - Philipp J. Jost
- III Medical Department for Hematology and Oncology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Christian Peschel
- III Medical Department for Hematology and Oncology, Klinikum Rechts der IsarTechnische Universität München Munich Germany
| | - Justus Duyster
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Timo Gaiser
- Institute of Pathology, University Medical Center MannheimRuprecht‐Karl University of Heidelberg Mannheim Germany
| | - Peter Hohenberger
- Division of Surgical Oncology and Thoracic SurgeryUniversity Medical Center Mannheim, Ruprecht‐Karl University of Heidelberg Mannheim Germany
| | - Nikolas Bubnoff
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Hematology and Oncology, Medical CenterUniversity of Schleswig Holstein Lübeck Germany
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23
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Deans ZC, Butler R, Cheetham M, Dequeker EMC, Fairley JA, Fenizia F, Hall JA, Keppens C, Normanno N, Schuuring E, Patton SJ. IQN path ASBL report from the first European cfDNA consensus meeting: expert opinion on the minimal requirements for clinical ctDNA testing. Virchows Arch 2019; 474:681-689. [PMID: 31028539 PMCID: PMC6581928 DOI: 10.1007/s00428-019-02571-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 02/08/2019] [Accepted: 04/02/2019] [Indexed: 12/18/2022]
Abstract
Liquid biopsy testing is a new laboratory-based method that detects tumour mutations in circulating free DNA (cfDNA) derived from minimally invasive blood sampling techniques. Recognising the significance for clinical testing, in 2017, IQN Path provided external quality assessment for liquid biopsy testing. Representatives of those participating laboratories were invited to attend a workshop to discuss the findings and how to achieve quality implementation of cfDNA testing in the clinical setting, the discussion and outcomes of this consensus meeting are described below. Predictive molecular profiling using tumour tissue in order to select cancer patients eligible for targeted therapy is now routine in diagnostic pathology. If insufficient tumour tissue material is available, in some circumstances, recent European Medicines Agency (EMA) guidance recommends mutation testing with plasma cfDNA. Clinical applications of cfDNA include treatment selection based on clinically relevant mutations derived from pre-treatment samples and the detection of resistant mutations upon progression of the disease. In order to identify tumour-related mutations in amongst other nucleic acid material found in plasma samples, highly sensitive laboratory methods are needed. In the workshop, we discussed the variable approaches taken with regard to cfDNA extraction methods, the tests, and considered the impact of false-negative test results. We explored the lack of standardisation of complex testing procedures ranging from plasma collection, transport, processing and storage, cfDNA extraction, and mutation analysis, to interpretation and reporting of results. We will also address the current status of clinical validation and clinical utility, and its use in current diagnosis. This workshop revealed a need for guidelines on with standardised procedures for clinical cfDNA testing and reporting, and a requirement for cfDNA-based external quality assessment programs.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK.
| | - Rachel Butler
- All Wales Genetic Laboratory, Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Melanie Cheetham
- European Molecular Genetics Quality Network, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, M13 9WL, UK
| | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,University Hospital of Leuven, Leuven, Belgium
| | - Jennifer A Fairley
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Francesca Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Jacqueline A Hall
- International Quality Network for Pathology (IQN Path ASBL), 3A Sentier de l'Esperance, 1474, Luxembourg, Luxembourg
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands
| | - Simon J Patton
- European Molecular Genetics Quality Network, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, M13 9WL, UK
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24
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Ravegnini G, Sammarini G, Serrano C, Nannini M, Pantaleo MA, Hrelia P, Angelini S. Clinical relevance of circulating molecules in cancer: focus on gastrointestinal stromal tumors. Ther Adv Med Oncol 2019; 11:1758835919831902. [PMID: 30854029 PMCID: PMC6399766 DOI: 10.1177/1758835919831902] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/30/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, growing research interest has focused on the so-called liquid biopsy. A simple blood test offers access to a plethora of information, which might be extremely helpful in understanding or characterizing specific diseases. Blood contains different molecules, of which circulating free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs) and extracellular vesicles (EVs) are the most relevant. Conceivably, these molecules have the potential for tumor diagnosis, monitoring tumor evolution, and evaluating treatment response and pharmacological resistance. This review aims to present a state-of-the-art of recent advances in circulating DNA and circulating RNA in gastrointestinal stromal tumors (GISTs). To date, progress in liquid biopsy has been scarce in GISTs due to several issues correlated with the nature of the pathology. Namely, heterogeneity in primary and secondary mutations in key driver genes has greatly slowed the development and application in GISTs, unlike in other tumor types in which liquid biopsy has already been translated into clinical practice. However, meaningful novel data have shown in recent years a significant clinical potential of ctDNA, CTCs, EVs and circulating RNA in GISTs.
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Affiliation(s)
- Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Sammarini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - César Serrano
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Margherita Nannini
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Maria A Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, Via Irnerio 48, 40126 Bologna, Italy
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Boonstra PA, Ter Elst A, Tibbesma M, Gietema JA, Schuuring E, Reyners AKL. Diagnosis and Treatment Monitoring of a Patient with Gastrointestinal Stromal Tumor by Next-Generation Sequencing and Droplet Digital Polymerase Chain Reaction Assay of a PDGFRA Mutation in Plasma-Derived Cell-Free Tumor DNA. Oncologist 2019; 24:e387-e390. [PMID: 30670599 DOI: 10.1634/theoncologist.2018-0460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/26/2018] [Indexed: 01/16/2023] Open
Abstract
In patients with a suspected malignancy, standard-of care management currently includes histopathologic examination and analysis of tumor-specific molecular abnormalities. Herein, we present a 77-year-old patient with an abdominal mass suspected to be a gastrointestinal stromal tumor (GIST) but without the possibility to collect a tumor biopsy. Cell-free DNA extracted from a blood sample was analyzed for the presence of mutations in GIST-specific genes using next generation sequencing. Furthermore, liquid biopsies were used to monitor the levels of mutant DNA copies during treatment with a tumor-specific mutation droplet digital PCR assay that correlated with the clinical and radiological response. Blood-based testing is a good alternative for biopsy-based testing. However, it should only be applied when biopsies are not available or possible to obtain because overall, in only 50%-85% of the cell-free plasma samples is the known tumor mutation detected.
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Affiliation(s)
- Pieter A Boonstra
- Department of Medical Oncology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marco Tibbesma
- Department of Pathology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jourik A Gietema
- Department of Medical Oncology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anna K L Reyners
- Department of Medical Oncology, Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA. BMC Cancer 2018; 18:804. [PMID: 30092778 PMCID: PMC6085634 DOI: 10.1186/s12885-018-4694-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Molecular analysis of circulating tumour DNA (ctDNA) is becoming increasingly important in clinical treatment decisions. A pilot External Quality Assessment (EQA) scheme for ctDNA analysis was organized by four European EQA providers under the umbrella organization IQN Path, in order to investigate the feasibility of delivering an EQA to assess the detection of clinically relevant variants in plasma circulating cell-free DNA (cfDNA) and to analyze reporting formats. METHODS Thirty-two experienced laboratories received 5 samples for EGFR mutation analysis and/or 5 samples for KRAS and NRAS mutation analysis. Samples were artificially manufactured to contain 3 mL of human plasma with 20 ng/mL of fragmented ctDNA and variants at allelic frequencies of 1 and 5%. RESULTS The scheme error rate was 20.1%. Higher error rates were observed for RAS testing when compared to EGFR analysis, for allelic frequencies of 1% compared to 5%, and for cases including 2 different variants. The reports over-interpreted wild-type results and frequently failed to comment on the amount of cfDNA extracted. CONCLUSIONS The pilot scheme demonstrated the feasibility of delivering a ctDNA EQA scheme and the need for such a scheme due to high error rates in detecting low frequency clinically relevant variants. Recommendations to improve reporting of cfDNA are provided.
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