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van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, Deiman B, Huijsmans CJJ, van Eijk R, Speel EJM, van Haastert RJ, Ligtenberg MJL, van Schaik RHN, Jansen MPHM, Dubbink HJ, de Leng WW, Leers MPG, Tamminga M, van den Broek D, van Kempen LC, Schuuring E. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium. Clin Chem 2024; 70:759-767. [PMID: 38484302 DOI: 10.1093/clinchem/hvae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/21/2023] [Indexed: 05/03/2024]
Abstract
BACKGROUND Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands). METHODS Aliquots of 3 high-volume diagnostic leukapheresis (DLA) plasma samples and 3 artificial reference plasma samples with predetermined mutations were distributed among 16 Dutch laboratories. Participating laboratories were requested to perform ctDNA analysis for BRAF exon 15, EGFR exon 18-21, and KRAS exon 2-3 using their regular circulating cell-free DNA (ccfDNA) analysis work flow. Laboratories were assessed based on adherence to the study protocol, overall detection rate, and overall genotyping performance. RESULTS A broad range of preanalytical conditions (e.g., plasma volume, elution volume, and extraction methods) and analytical methodologies (e.g., droplet digital PCR [ddPCR], small-panel PCR assays, and next-generation sequencing [NGS]) were used. Six laboratories (38%) had a performance score of >0.90; all other laboratories scored between 0.26 and 0.80. Although 13 laboratories (81%) reached a 100% overall detection rate, the therapeutically relevant EGFR p.(S752_I759del) (69%), EGFR p.(N771_H773dup) (50%), and KRAS p.(G12C) (48%) mutations were frequently not genotyped accurately. CONCLUSIONS Divergent (pre)analytical protocols could lead to discrepant clinical outcomes when using the same plasma samples. Standardization of (pre)analytical work flows can facilitate the implementation of reproducible liquid biopsy testing in the clinical routine.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pim Rozendal
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - John Hinrichs
- Department of Pathology, Symbiant B.V., Alkmaar, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Karen Zwaenepoel
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Birgit Deiman
- Clinical Laboratory, Catharina Hospital Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Cornelis J J Huijsmans
- Pathologie-DNA, Laboratory for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rick J van Haastert
- Department of Clinical Chemistry, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pathology, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Laboratory of Translational Genomics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Wendy W de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mathie P G Leers
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Center, Heerlen, the Netherlands
| | - Menno Tamminga
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Lu T, Oomens L, Terstappen LWMM, Prakash J. In Vivo Detection of Circulating Cancer-Associated Fibroblasts in Breast Tumor Mouse Xenograft: Impact of Tumor Stroma and Chemotherapy. Cancers (Basel) 2023; 15:cancers15041127. [PMID: 36831470 PMCID: PMC9954095 DOI: 10.3390/cancers15041127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) are important drivers in the tumor microenvironment and facilitate the growth and survival of tumor cells, as well as metastasis formation. They may travel together with tumor cells to support their survival and aid in the formation of a metastatic niche. In this study, we aimed to study circulating CAFs (cCAFs) and circulating tumor cells (CTCs) in a preclinical breast tumor model in mice in order to understand the effect of chemotherapy on cCAFs and CTC formation. Tumors with MDA-MB-231 human breast tumor cells with/without primary human mammary fibroblasts (representing CAFs) were coinjected in SCID mice to develop tumors. We found that the tumors with CAFs grew faster than tumors without CAFs. To study the effect of the stroma on CTCs and cCAFs, we isolated cells using microsieve filtration technology and established ITGA5 as a new cCAF biomarker, which showed good agreement with the CAF markers FAP and α-SMA. We found that ITGA5+ cCAFs shed in the blood of mice bearing stroma-rich coinjection-based tumors, while there was no difference in CTC formation. Although treatment with liposomal doxorubicin reduced tumor growth, it increased the numbers of both cCAFs and CTCs in blood. Moreover, cCAFs and CTCs were found to form clusters in the chemotherapy-treated mice. Altogether, these findings indicate that the tumor stroma supports tumor growth and the formation of cCAFs. Furthermore, chemotherapy may exacerbate the formation of cCAFs and CTCs, which may eventually support the formation of a metastasis niche in breast cancer.
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Affiliation(s)
- Tao Lu
- Engineered Therapeutics, Department of Advanced Organ Bioengineering and Therapeutics, TechMed Centre, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, 7500 AE Enschede, The Netherlands
| | - Lisa Oomens
- VyCAP B.V., Capitool 41, 7521 PL Enschede, The Netherlands
| | - Leon W. M. M. Terstappen
- Medical Cell BioPhysics, Faculty of Science and Technology, University of Twente, Hallenweg 23, 7522 NH Enschede, The Netherlands
| | - Jai Prakash
- Engineered Therapeutics, Department of Advanced Organ Bioengineering and Therapeutics, TechMed Centre, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, 7500 AE Enschede, The Netherlands
- Correspondence:
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Assessment of a Size-Based Method for Enriching Circulating Tumour Cells in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14143446. [PMID: 35884509 PMCID: PMC9319975 DOI: 10.3390/cancers14143446] [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: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 12/07/2022] Open
Abstract
Circulating tumour cells (CTC) from solid tumours are a prerequisite for metastasis. Isolating CTCs and understanding their biology is essential for developing new clinical tests and precision oncology. Currently, CellSearch is the only FDA (U.S. Food and Drug Administration)-approved method for CTC enrichment but possesses several drawbacks owing to a reliance on the epithelial cell adhesion molecule (EpCAM) and a resource-intensive nature. Addressing these shortcomings, we optimised an existing size-based method, MetaCell, to enrich CTCs from blood of colorectal cancer (CRC) patients. We evaluated the ability of MetaCell to enrich CTCs by spiking blood with CRC cell lines and assessing the cell recovery rates and WBC depletion via immunostaining and gene expression. We then applied MetaCell to samples from 17 CRC patients and seven controls. Recovery rates were >85% in cell lines, with >95% depletion in WBCs. MetaCell yielded CTCs and CTC clusters in 52.9% and 23.5% of the patients, respectively, without false positives in control patients. CTCs and cluster detection did not correlate with histopathological parameters. Overall, we demonstrated that the MetaCell platform enriched CRC cells with high recovery rates and high purity. Our pilot study also demonstrated the ability of MetaCell to detect CTCs in CRC patients.
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Weber S, Spiegl B, Perakis SO, Ulz CM, Abuja PM, Kashofer K, van der Leest P, Azpurua MA, Tamminga M, Brudzewsky D, Rothwell DG, Mohan S, Sartori A, Lampignano R, Konigshofer Y, Sprenger-Haussels M, Wikman H, Bergheim IR, Kloten V, Schuuring E, Speicher MR, Heitzer E. Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling. Cancers (Basel) 2020; 12:E1588. [PMID: 32560092 PMCID: PMC7352370 DOI: 10.3390/cancers12061588] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.
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Affiliation(s)
- Sabrina Weber
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
| | - Benjamin Spiegl
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Samantha O. Perakis
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Christine M. Ulz
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Peter M. Abuja
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Karl Kashofer
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Paul van der Leest
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Maria Aguirre Azpurua
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Menno Tamminga
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Dan Brudzewsky
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | - Dominic G. Rothwell
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | - Sumitra Mohan
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | | | - Rita Lampignano
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Yves Konigshofer
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany;
| | - Inger R. Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, N-0310 Oslo, Norway;
| | - Vera Kloten
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
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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: 36] [Impact Index Per Article: 9.0] [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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