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Helmijr J, Motta G, Jongbloed L, de Weerd V, van Bergen L, Verschoor N, Stella S, Beaufort C, Vigneri P, Martens JWM, Wilting SM, Jansen MPHM. A Multiplex Assay for Fast PIK3CA Hotspot Mutation Characterization in a Single Specimen by 3-Color Digital PCR Analysis. J Appl Lab Med 2024:jfae064. [PMID: 39012846 DOI: 10.1093/jalm/jfae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/01/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Activating mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene have been detected often in solid tumors. Targeted therapy for mutant PIK3CA is now available in the clinic, making molecular diagnostics pivotal. Our aim was to design a multiplex digital PCR (dPCR) assay to evaluate the 4 most common PIK3CA hotspot mutations simultaneously to characterize and quantify these in liquid biopsies. METHODS A multiplex assay was developed to detect exon 9 p.E542K and p.E545K mutations, and exon 20 p.H1047L and p.H1047R mutations using the Stilla 3-color dPCR Naica system. The assay was evaluated on stock and pre-amplified DNA from cell lines with the above mutations as single and pooled samples, and on cell-free DNA (cfDNA) from healthy blood donors (HBDs) and breast cancer patients, to determine detection thresholds and diagnostic accuracy. RESULTS The assay distinguished all 4 PIK3CA mutations in (cf)DNA, and also when dual mutations were present. Detection thresholds of stock and pre-amplified cfDNA samples were 0.11 and 0.40 copies/uL (cp/uL) for mutant copies concentration, and 0.003% and 0.68% for variant allele frequencies (VAFs), respectively. The assay confirmed the PIK3CA (mutation) status as defined by targeted next-generation sequencing (NGS) in 82 out of 96 patients that were mutant for PIK3CA, and in 11 out of 12 patients with wild-type PIK3CA. CONCLUSIONS Our designed multiplex dPCR assay detected PIK3CA mutations with high accuracy in stock and pre-amplified cfDNA. Furthermore, it is affordable and demands less cfDNA input when compared to available uniplex dPCR assays and NGS analyses.
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Affiliation(s)
- Jean Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Gianmarco Motta
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
- Department of Clinical and Experimental Medicine, Center for Experimental Oncology and Hematology, University of Catania, Catania, Italy
| | - Lisa Jongbloed
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Lotte van Bergen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Stefania Stella
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
- Department of Clinical and Experimental Medicine, Center for Experimental Oncology and Hematology, University of Catania, Catania, Italy
| | - Corine Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, Center for Experimental Oncology and Hematology, University of Catania, Catania, Italy
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, the Netherlands
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2
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Venetis K, Pepe F, Pescia C, Cursano G, Criscitiello C, Frascarelli C, Mane E, Russo G, Taurelli Salimbeni B, Troncone G, Guerini Rocco E, Curigliano G, Fusco N, Malapelle U. ESR1 mutations in HR+/HER2-metastatic breast cancer: Enhancing the accuracy of ctDNA testing. Cancer Treat Rev 2023; 121:102642. [PMID: 37864956 DOI: 10.1016/j.ctrv.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Activating mutations of the estrogen receptor alpha gene (ESR1) are common mechanisms of endocrine therapy (ET) resistance in hormone receptor-positive (HR + )/Human Epidermal Growth Factor Receptor 2 (HER2)-negative metastatic breast cancer (MBC). Recent clinical findings emphasize that both old and new generations of selective ER degraders (SERDs) demonstrate enhanced clinical effectiveness in patients with MBC who have detectable ESR1 mutations via liquid biopsy. This stands in contrast to individuals with MBC carrying these mutations and undergoing conventional endocrine monotherapies like aromatase inhibitors (AIs). Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has emerged as a promising, minimally invasive alternative to conventional tissue-based testing for identifying ESR1 mutations. Within the context of the PADA-1 and EMERALD trials, distinct molecular methodologies and assays, specifically digital droplet PCR (ddPCR) and next-generation sequencing (NGS), have been employed to evaluate the mutational status of ESR1 within ctDNA. This manuscript critically examines the advantages and indications of various ctDNA testing methods on liquid biopsy for HR+/HER2-negative MBC. Specifically, we delve into the capabilities of ddPCR and NGS in identifying ESR1 mutations. Each methodology boasts unique strengths and limitations: ddPCR excels in its analytical sensitivity for pinpointing hotspot mutations, while NGS offers comprehensive coverage of the spectrum of ESR1 mutations. The significance of meticulous sample handling and timely analysis is emphasized, acknowledging the transient nature of cfDNA. Furthermore, we underscore the importance of detecting sub-clonal ESR1 mutations, as these variants can exert a pivotal influence on predicting both endocrine therapy resistance and responsiveness to SERDs. In essence, this work discusses the role of ctDNA analysis for detecting ESR1 mutations and their implications in tailoring effective therapeutic strategies for HR+/HER2- MBC.
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Affiliation(s)
| | - Francesco Pepe
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; School of Pathology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Eltjona Mane
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gianluca Russo
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | | | - Giancarlo Troncone
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Naples, Italy
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3
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Ranghiero A, Frascarelli C, Cursano G, Pescia C, Ivanova M, Vacirca D, Rappa A, Taormina SV, Barberis M, Fusco N, Rocco EG, Venetis K. Circulating tumour DNA testing in metastatic breast cancer: Integration with tissue testing. Cytopathology 2023; 34:519-529. [PMID: 37640801 DOI: 10.1111/cyt.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
Breast cancer biomarker profiling predominantly relies on tissue testing (surgical and/or biopsy samples). However, the field of liquid biopsy, particularly the analysis of circulating tumour DNA (ctDNA), has witnessed remarkable progress and continues to evolve rapidly. The incorporation of ctDNA-based testing into clinical practice is creating new opportunities for patients with metastatic breast cancer (MBC). ctDNA offers advantages over conventional tissue analyses, as it reflects tumour heterogeneity and enables multiple serial biopsies in a minimally invasive manner. Thus, it serves as a valuable complement to standard tumour tissues and, in certain instances, may even present a potential alternative approach. In the context of MBC, ctDNA testing proves highly informative in the detection of disease progression, monitoring treatment response, assessing actionable biomarkers, and identifying mechanisms of resistance. Nevertheless, ctDNA does exhibit inherent limitations, including its generally low abundance, necessitating timely blood samplings and rigorous management of the pre-analytical phase. The development of highly sensitive assays and robust bioinformatic tools has paved the way for reliable ctDNA analyses. The time has now come to establish how ctDNA and tissue analyses can be effectively integrated into the diagnostic workflow of MBC to provide patients with the most comprehensive and accurate profiling. In this manuscript, we comprehensively analyse the current methodologies employed in ctDNA analysis and explore the potential benefits arising from the integration of tissue and ctDNA testing for patients diagnosed with MBC.
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Affiliation(s)
- Alberto Ranghiero
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- School of Pathology, University of Milan, Milan, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Massimo Barberis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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5
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Jongbloed EM, Jansen MPHM, de Weerd V, Helmijr JA, Beaufort CM, Reinders MJT, van Marion R, van IJcken WFJ, Sonke GS, Konings IR, Jager A, Martens JWM, Wilting SM, Makrodimitris S. Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels. Sci Rep 2023; 13:10424. [PMID: 37369746 DOI: 10.1038/s41598-023-37409-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023] Open
Abstract
Next generation sequencing of cell-free DNA (cfDNA) is a promising method for treatment monitoring and therapy selection in metastatic breast cancer (MBC). However, distinguishing tumor-specific variants from sequencing artefacts and germline variation with low false discovery rate is challenging when using large targeted sequencing panels covering many tumor suppressor genes. To address this, we built a machine learning model to remove false positive variant calls and augmented it with additional filters to ensure selection of tumor-derived variants. We used cfDNA of 70 MBC patients profiled with both the small targeted Oncomine breast panel (Thermofisher) and the much larger Qiaseq Human Breast Cancer Panel (Qiagen). The model was trained on the panels' common regions using Oncomine hotspot mutations as ground truth. Applied to Qiaseq data, it achieved 35% sensitivity and 36% precision, outperforming basic filtering. For 20 patients we used germline DNA to filter for somatic variants and obtained 245 variants in total, while our model found seven variants, of which six were also detected using the germline strategy. In ten tumor-free individuals, our method detected in total one (potentially germline) variant, in contrast to 521 variants detected without our model. These results indicate that our model largely detects somatic variants.
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Affiliation(s)
- Elisabeth M Jongbloed
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Inge R Konings
- Department of Medical Oncology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stavros Makrodimitris
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
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Vitale SR, Ruigrok-Ritstier K, Timmermans AM, Foekens R, Trapman-Jansen AMAC, Beaufort CM, Vigneri P, Sleijfer S, Martens JWM, Sieuwerts AM, Jansen MPHM. The prognostic and predictive value of ESR1 fusion gene transcripts in primary breast cancer. BMC Cancer 2022; 22:165. [PMID: 35151276 PMCID: PMC8840267 DOI: 10.1186/s12885-022-09265-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background In breast cancer (BC), recurrent fusion genes of estrogen receptor alpha (ESR1) and AKAP12, ARMT1 and CCDC170 have been reported. In these gene fusions the ligand binding domain of ESR1 has been replaced by the transactivation domain of the fusion partner constitutively activating the receptor. As a result, these gene fusions can drive tumor growth hormone independently as been shown in preclinical models, but the clinical value of these fusions have not been reported. Here, we studied the prognostic and predictive value of different frequently reported ESR1 fusion transcripts in primary BC. Methods We evaluated 732 patients with primary BC (131 ESR1-negative and 601 ESR1-positive cases), including two ER-positive BC patient cohorts: one cohort of 322 patients with advanced disease who received first-line endocrine therapy (ET) (predictive cohort), and a second cohort of 279 patients with lymph node negative disease (LNN) who received no adjuvant systemic treatment (prognostic cohort). Fusion gene transcript levels were measured by reverse transcriptase quantitative PCR. The presence of the different fusion transcripts was associated, in uni- and multivariable Cox regression analysis taking along current clinico-pathological characteristics, to progression free survival (PFS) during first-line endocrine therapy in the predictive cohort, and disease- free survival (DFS) and overall survival (OS) in the prognostic cohort. Results The ESR1-CCDC170 fusion transcript was present in 27.6% of the ESR1-positive BC subjects and in 2.3% of the ESR1-negative cases. In the predictive cohort, none of the fusion transcripts were associated with response to first-line ET. In the prognostic cohort, the median DFS and OS were respectively 37 and 93 months for patients with an ESR1-CCDC170 exon 8 gene fusion transcript and respectively 91 and 212 months for patients without this fusion transcript. In a multivariable analysis, this ESR1-CCDC170 fusion transcript was an independent prognostic factor for DFS (HR) (95% confidence interval (CI): 1.8 (1.2–2.8), P = 0.005) and OS (HR (95% CI: 1.7 (1.1–2.7), P = 0.023). Conclusions Our study shows that in primary BC only ESR1-CCDC170 exon 8 gene fusion transcript carries prognostic value. None of the ESR1 fusion transcripts, which are considered to have constitutive ER activity, was predictive for outcome in BC with advanced disease treated with endocrine treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09265-1.
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7
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Deger T, Boers RG, de Weerd V, Angus L, van der Put MMJ, Boers JB, Azmani Z, van IJcken WFJ, Grünhagen DJ, van Dessel LF, Lolkema MPJK, Verhoef C, Sleijfer S, Martens JWM, Gribnau J, Wilting SM. High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments. Clin Epigenetics 2021; 13:196. [PMID: 34670587 PMCID: PMC8529776 DOI: 10.1186/s13148-021-01177-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023] Open
Abstract
Background DNA methylation detection in liquid biopsies provides a highly promising and much needed means for real-time monitoring of disease load in advanced cancer patient care. Compared to the often-used somatic mutations, tissue- and cancer-type specific epigenetic marks affect a larger part of the cancer genome and generally have a high penetrance throughout the tumour. Here, we describe the successful application of the recently described MeD-seq assay for genome-wide DNA methylation profiling on cell-free DNA (cfDNA). The compatibility of the MeD-seq assay with different types of blood collection tubes, cfDNA input amounts, cfDNA isolation methods, and vacuum concentration of samples was evaluated using plasma from both metastatic cancer patients and healthy blood donors (HBDs). To investigate the potential value of cfDNA methylation profiling for tumour load monitoring, we profiled paired samples from 8 patients with resectable colorectal liver metastases (CRLM) before and after surgery. Results The MeD-seq assay worked on plasma-derived cfDNA from both EDTA and CellSave blood collection tubes when at least 10 ng of cfDNA was used. From the 3 evaluated cfDNA isolation methods, both the manual QIAamp Circulating Nucleic Acid Kit (Qiagen) and the semi-automated Maxwell® RSC ccfDNA Plasma Kit (Promega) were compatible with MeD-seq analysis, whereas the QiaSymphony DSP Circulating DNA Kit (Qiagen) yielded significantly fewer reads when compared to the QIAamp kit (p < 0.001). Vacuum concentration of samples before MeD-seq analysis was possible with samples in AVE buffer (QIAamp) or water, but yielded inconsistent results for samples in EDTA-containing Maxwell buffer. Principal component analysis showed that pre-surgical samples from CRLM patients were very distinct from HBDs, whereas post-surgical samples were more similar. Several described methylation markers for colorectal cancer monitoring in liquid biopsies showed differential methylation between pre-surgical CRLM samples and HBDs in our data, supporting the validity of our approach. Results for MSC, ITGA4, GRIA4, and EYA4 were validated by quantitative methylation specific PCR. Conclusions The MeD-seq assay provides a promising new method for cfDNA methylation profiling. Potential future applications of the assay include marker discovery specifically for liquid biopsy analysis as well as direct use as a disease load monitoring tool in advanced cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01177-4.
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Affiliation(s)
- Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marjolijn M J van der Put
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Z Azmani
- Center for Biomics, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Dirk J Grünhagen
- Department of Oncologic Surgery, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Lisanne F van Dessel
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Martijn P J K Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Cornelis Verhoef
- Department of Oncologic Surgery, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands.
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8
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A Systematic Review of the Use of Circulating Cell-Free DNA Dynamics to Monitor Response to Treatment in Metastatic Breast Cancer Patients. Cancers (Basel) 2021; 13:cancers13081811. [PMID: 33920135 PMCID: PMC8069506 DOI: 10.3390/cancers13081811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/24/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
Monitoring treatment response in metastatic breast cancer currently consists mainly of radiological and clinical assessments. These methods have high inter-observer variation, suboptimal sensitivity to determine response to treatment and give little insight into the biological characteristics of the tumor. Assessing circulating tumor DNA (ctDNA) over time could be employed to address these limitations. Several ways to quantify and characterize ctDNA exist, based on somatic mutations, copy number variations, methylation, and global circulating cell-free DNA (cfDNA) fragment sizes and concentrations. These methods are being explored and technically validated, but to date none of these methods are applied clinically. We systematically reviewed the literature on the use of quantitative ctDNA measurements over time to monitor response to systemic therapy in patients with metastatic breast cancer. Cochrane, Embase, PubMed and Google Scholar databases were searched to find studies focusing on the use of cfDNA to longitudinally monitor treatment response in advanced breast cancer patients until October 2020. This resulted in a total of 33 studies which met the inclusion criteria. These studies were heterogeneous in (pre-)processing procedures, applied techniques and design. An association between ctDNA and treatment response was found in most of the included studies, independent of the applied assay. To implement ctDNA-based response monitoring into daily clinical practice for metastatic breast cancer patients, sample (pre-) processing procedures need to be standardized and large prospectively collected sample cohorts with well annotated clinical follow-up are required to establish its clinical validity.
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Fundamentals of liquid biopsies in metastatic prostate cancer: from characterization to stratification. Curr Opin Oncol 2020; 32:527-534. [PMID: 32675591 DOI: 10.1097/cco.0000000000000655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW In this review, we provide an overview of the recent developments and prospects on the applications of blood-based liquid biopsies, including circulating tumor DNA and circulating tumor cells, in metastatic prostate cancer. RECENT FINDINGS Guidelines and consensus statements have been formulated to standardize preanalytical conditions that affect liquid biopsy analysis. Currently, there are four FDA approved assays for the analysis of liquid biopsies and many quantitative and qualitative assays are being developed. Comprehensive analyses of cell-free tumor DNA (ctDNA) and circulating tumor cells (CTCs) demonstrate that they adequately reflect the genomic makeup of the tumor and may thus complement or even replace tumor biopsies. The assessment of genomic aberrations in ctDNA can potentially predict therapy response and detect mechanisms of resistance. CTC count is not only a strong prognosticator in metastatic prostate cancer but can also measure therapy response. SUMMARY Liquid biopsies may provide a temporal snapshot of the biologic variables that affect tumor growth and progression in metastatic prostate cancer. Liquid biopsies could inform on prognostic, predictive, and response measures. However, prospective clinical trials need to be performed to provide definitive validation of the clinical value of the most advanced assays.
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Liao H, Li H. Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer. Cancer Manag Res 2020; 12:3547-3560. [PMID: 32547192 PMCID: PMC7244344 DOI: 10.2147/cmar.s249041] [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: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
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Vitale SR, Groenendijk FH, van Marion R, Beaufort CM, Helmijr JC, Jan Dubbink H, N. M. Dinjens W, Ewing-Graham PC, Smolders R, van Doorn HC, Boere IA, Berns EMJJ, Helleman J, Jansen MPHM. TP53 Mutations in Serum Circulating Cell-Free Tumor DNA As Longitudinal Biomarker for High-Grade Serous Ovarian Cancer. Biomolecules 2020; 10:biom10030415. [PMID: 32156073 PMCID: PMC7175353 DOI: 10.3390/biom10030415] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/06/2020] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was used for baseline cfDNAs. TP53 missense mutations were observed in 17 tissue specimens and in baseline cfDNA for 4/8 patients by AmpliSeq, 6/9 patients by Oncomine, and 4/6 patients by dPCR. Mutations in cfDNA were detected in 4/6 patients with residual disease and 3/4 patients with disease progression within six months, compared to 5/11 patients with no residual disease and 6/13 patients with progression after six months. Finally, mutations were detected at progression in 5/6 patients, but not during chemotherapy. NGS with molecular barcoding and dPCR were most optimal workflows to detect TP53 mutations in baseline and longitudinal serum cfDNA, respectively. TP53 mutations were undetectable in cfDNA during treatment but re-appeared at disease progression, illustrating its promise as a biomarker for disease monitoring.
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Affiliation(s)
- Silvia R. Vitale
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, 95123 Catania, Italy
- Correspondence: ; Tel.: +39-095-3781946
| | - Floris H. Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Corine M. Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jean C. Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Hendrikus Jan Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Patricia C. Ewing-Graham
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ramon Smolders
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Helena C. van Doorn
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Ingrid A. Boere
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Els M. J. J. Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jozien Helleman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Maurice P. H. M. Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
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Kruger DT, Jansen MPHM, Konings IRHM, Dercksen WM, Jager A, Oulad Hadj J, Sleijfer S, Martens JWM, Boven E. High ctDNA molecule numbers relate with poor outcome in advanced ER+, HER2- postmenopausal breast cancer patients treated with everolimus and exemestane. Mol Oncol 2020; 14:490-503. [PMID: 31841262 PMCID: PMC7053245 DOI: 10.1002/1878-0261.12617] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/28/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022] Open
Abstract
We determined whether progression‐free survival (PFS) in metastatic breast cancer (MBC) patients receiving everolimus plus exemestane (EVE/EXE) varies depending on circulating tumour DNA (ctDNA) characteristics. Baseline plasma cell‐free DNA (cfDNA) from 164 postmenopausal women with ER‐positive, HER2‐negative MBC refractory to a nonsteroidal aromatase inhibitor and treated with standard EVE/EXE (Everolimus Biomarker Study, Eudract 2013‐004120‐11) was characterised for 10 relevant breast cancer genes by next‐generation sequencing with molecular barcoding. ctDNA molecule numbers, number of mutations and specific variants were related with PFS and overall survival (OS). Missense hotspot mutations in cfDNA were detected in 125 patients. The median of 54 ctDNA molecules per mL plasma distinguished patients with high and low/no ctDNA load. Patients with low/no ctDNA load (N = 102) showed longer median PFS of 5.7 months (P = 0.006) and OS of 124.8 months (P = 0.008) than patients with high ctDNA load (N = 62; 4.4 months and 107.7 months, respectively) in multivariate analyses. Patients with < 3 specific mutations (N = 135) had longer median PFS of 5.4 months compared to those with ≥ 3 mutations (3.4 months; P < 0.001). In conclusion, MBC patients with low/no ctDNA load or < 3 hotspot mutations experience longer PFS while treated with EVE/EXE.
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Affiliation(s)
- Dinja T Kruger
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Inge R H M Konings
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, The Netherlands
| | - Wouter M Dercksen
- Department of Medical Oncology, Maxima Medical Centre, Eindhoven, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jamal Oulad Hadj
- Department of Medical Oncology, Gelre Ziekenhuis, Apeldoorn, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Epie Boven
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, The Netherlands
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