1
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Klocker EV, Hasenleithner S, Bartsch R, Gampenrieder SP, Egle D, Singer CF, Rinnerthaler G, Hubalek M, Schmitz K, Bago-Horvath Z, Petzer A, Heibl S, Heitzer E, Balic M, Gnant M. Clinical applications of next-generation sequencing-based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression. Mol Oncol 2024. [PMID: 38867388 DOI: 10.1002/1878-0261.13671] [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: 11/02/2023] [Revised: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non-invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real-time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.
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Affiliation(s)
- Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Simon P Gampenrieder
- Third Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Austria
| | - Daniel Egle
- Department of Gynecology, Breast Cancer Center Tirol, Medical University of Innsbruck, Austria
| | - Christian F Singer
- Department of Gynecology, Breast Cancer Center Vienna, Medical University of Vienna, Austria
| | - Gabriel Rinnerthaler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Michael Hubalek
- Department of Gynecology, Breast Health Center Schwaz, Austria
| | - Katja Schmitz
- Institute of Pathology, University Medical Center Göttingen, Germany
- Tyrolpath Obrist Brunhuber GmbH and Krankenhaus St. Vinzenz, Zams, Austria
| | | | - Andreas Petzer
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Barmherzige Schwestern, Elisabethinen, Ordensklinikum Linz GmbH, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen GmbH, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Christian Doppler Laboratory for Liquid Biopsies for early Detection of Cancer, Medical University of Graz, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
- Division of Hematology and Medical Oncology, University of Pittsburgh School of Medicine, PA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Austria
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2
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Nicolò E, Gianni C, Pontolillo L, Serafini MS, Munoz-Arcos LS, Andreopoulou E, Curigliano G, Reduzzi C, Cristofanilli M. Circulating tumor cells et al.: towards a comprehensive liquid biopsy approach in breast cancer. TRANSLATIONAL BREAST CANCER RESEARCH : A JOURNAL FOCUSING ON TRANSLATIONAL RESEARCH IN BREAST CANCER 2024; 5:10. [PMID: 38751670 PMCID: PMC11093063 DOI: 10.21037/tbcr-23-55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Liquid biopsy has emerged as a crucial tool in managing breast cancer (BC) patients, offering a minimally invasive approach to detect circulating tumor biomarkers. Until recently, the majority of the studies in BC focused on evaluating a single liquid biopsy analyte, primarily circulating tumor DNA and circulating tumor cells (CTCs). Despite the proven prognostic and predictive value of CTCs, their low abundance when detected using enrichment methods, especially in the early stages, poses a significant challenge. It is becoming evident that combining diverse circulating biomarkers, each representing different facets of tumor biology, has the potential to enhance the management of patients with BC. This article emphasizes the importance of considering these biomarkers as complementary/synergistic rather than competitive, recognizing their ability to contribute to a comprehensive disease profile. The review provides an overview of the clinical significance of simultaneously analyzing CTCs and other biomarkers, including cell-free circulating DNA, extracellular vesicles, non-canonical CTCs, cell-free RNAs, and non-malignant cells. Such a comprehensive liquid biopsy approach holds promise not only in BC but also in other cancer types, offering opportunities for early detection, prognostication, and therapy monitoring. However, addressing associated challenges, such as refining detection methods and establishing standardized protocols, is crucial for realizing the full potential of liquid biopsy in transforming our understanding and approach to BC. As the field evolves, collaborative efforts will be instrumental in unlocking the revolutionary impact of liquid biopsy in BC research and management.
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Affiliation(s)
- Eleonora Nicolò
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Caterina Gianni
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Letizia Pontolillo
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Medical Oncology Department, Catholic University of Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Mara Serena Serafini
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Laura Sofia Munoz-Arcos
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Eleni Andreopoulou
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giuseppe Curigliano
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
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3
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [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: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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4
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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5
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Isebia KT, Mostert B, Deger T, Kraan J, de Weerd V, Oomen‐de Hoop E, Hamberg P, Haberkorn BCM, Helgason HH, de Wit R, Mathijssen RHJ, Lolkema MP, Wilting SM, van Riet J, Martens JWM. mFast-SeqS-based aneuploidy score in circulating cell-free DNA is a prognostic biomarker in prostate cancer. Mol Oncol 2023; 17:1898-1907. [PMID: 37178439 PMCID: PMC10483599 DOI: 10.1002/1878-0261.13449] [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: 01/19/2023] [Revised: 04/13/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023] Open
Abstract
Multiple prognostic biomarkers, including circulating tumour cell (CTC) counts, exist in metastatic castration-resistant prostate cancer (mCRPC) patients, but none of them have been implemented into daily clinical care. The modified fast aneuploidy screening test-sequencing system (mFast-SeqS), which yields a genome-wide aneuploidy score, is able to reflect the fraction of cell-free tumour DNA (ctDNA) within cell-free DNA (cfDNA) and may be a promising biomarker in mCRPC. In this study, we investigated the prognostic value of dichotomized aneuploidy scores (< 5 vs. ≥ 5) as well as CTC counts (< 5 vs. ≥ 5) in 131 mCRPC patients prior to treatment with cabazitaxel. We validated our findings in an independent cohort of 50 similarly treated mCRPC patients. We observed that, similar to the dichotomized CTC count [HR: 2.92; 95% confidence interval (CI);1.84-4.62], dichotomized aneuploidy scores (HR: 3.24; CI: 2.12-4.94) significantly correlated with overall survival in mCRPC patients. We conclude that a dichotomized aneuploidy score from cfDNA is a prognostic marker for survival in mCRPC patients within our discovery cohort and in an independent mCRPC validation cohort. Therefore, this easy and robust minimally-invasive assay can be readily implemented as a prognostic marker in mCRPC. A dichotomized aneuploidy score might also be used as a stratification factor in clinical studies to account for tumour load.
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Affiliation(s)
- Khrystany T. Isebia
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Esther Oomen‐de Hoop
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Paul Hamberg
- Department of Internal MedicineFranciscus Gasthuis & VlietlandRotterdam/SchiedamThe Netherlands
| | | | - Helgi H. Helgason
- Department of Medical OncologyHaaglanden Medical CentreThe HagueThe Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Ron H. J. Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Martijn P. Lolkema
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer InstituteUniversity Medical Center RotterdamThe Netherlands
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6
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Verschoor N, de Weerd V, Van MN, Kraan J, Smid M, Heijns JB, Drooger JC, Zuetenhorst JM, van der Padt-Pruijsten A, Jager A, Sleijfer S, Martens JWM, Wilting SM. Tumor-agnostic ctDNA levels by mFAST-SeqS in first-line HR-positive, HER2 negative metastatic breast cancer patients as a biomarker for survival. NPJ Breast Cancer 2023; 9:61. [PMID: 37452019 PMCID: PMC10349058 DOI: 10.1038/s41523-023-00563-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
This prospective cohort study reports aneuploidy score by mFast-SeqS as a strong prognostic marker in MBC patients. mFAST-SeqS is an affordable and easily implementable method for the assessment of total ctDNA levels and, as such, provides an alternative prognostic tool. One mixed cohort (cohort A, n = 45) starting any type of treatment in any line of therapy and one larger cohort (cohort B, n = 129) consisting of patients starting aromatase inhibitors (AI) as first-line therapy were used. mFAST-SeqS was performed using plasma of blood in which CTCs (CellSearch) were enumerated. The resulting aneuploidy score was correlated with categorized CTC count and associated with outcome. The aneuploidy score was significantly correlated with CTC count, but discordance was observed in 31.6% when applying cut-offs of 5. In both cohorts, aneuploidy score was a significant prognostic marker for both PFS and OS. In the Cox regression models, the HR for aneuploidy score for PFS was 2.52 (95% CI: 1.56-4.07), and the HR for OS was 2.37 (95% CI: 1.36-4.14). Results presented here warrant further investigations into the clinical utility of this marker in MBC patients.
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Affiliation(s)
- Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mai N Van
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joan B Heijns
- Department of Medical Oncology, Amphia, Breda, The Netherlands
| | - Jan C Drooger
- Department of Medical Oncology, Breast Cancer Center South Holland South, Ikazia Hospital, Rotterdam, The Netherlands
| | - Johanna M Zuetenhorst
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, Rotterdam/ Schiedam, the Netherlands
| | | | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, 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
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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7
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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8
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Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12040870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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9
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Zhou Q, Gampenrieder SP, Frantal S, Rinnerthaler G, Singer CF, Egle D, Pfeiler G, Bartsch R, Wette V, Pichler A, Petru E, Dubsky PC, Bago-Horvath Z, Fesl C, Rudas M, Ståhlberg A, Graf R, Weber S, Dandachi N, Filipits M, Gnant M, Balic M, Heitzer E. Persistence of ctDNA in Patients with Breast Cancer During Neoadjuvant Treatment Is a Significant Predictor of Poor Tumor Response. Clin Cancer Res 2022; 28:697-707. [PMID: 34862246 PMCID: PMC9377752 DOI: 10.1158/1078-0432.ccr-21-3231] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Accurate response assessment during neoadjuvant systemic treatment (NST) poses a clinical challenge. Therefore, a minimally invasive assessment of tumor response based on cell-free circulating tumor DNA (ctDNA) may be beneficial to guide treatment decisions. EXPERIMENTAL DESIGN We profiled 93 genes in tissue from 193 patients with early breast cancer. Patient-specific assays were designed for 145 patients to track ctDNA during NST in plasma. ctDNA presence and levels were correlated with complete pathological response (pCR) and residual cancer burden (RCB) as well as clinicopathologic characteristics of the tumor to identify potential proxies for ctDNA release. RESULTS At baseline, ctDNA could be detected in 63/145 (43.4%) patients and persisted in 25/63 (39.7%) patients at mid-therapy (MT) and 15/63 (23.8%) patients at the end of treatment. ctDNA detection at MT was significantly associated with higher RCB (OR = 0.062; 95% CI, 0.01-0.48; P = 0.0077). Of 31 patients with detectable ctDNA at MT, 30 patients (96.8%) were nonresponders (RCB II, n = 8; RCB III, n = 22) and only one patient responded to the treatment (RCB I). Considering all 145 patients with baseline (BL) plasma, none of the patients with RCB 0 and only 6.7% of patients with RCB I had ctDNA detectable at MT, whereas 30.6% and 29.6% of patients with RCB II/III, respectively, had a positive ctDNA result. CONCLUSIONS Overall, our results demonstrate that the detection and persistence of ctDNA at MT may have the potential to negatively predict response to neoadjuvant treatment and identify patients who will not achieve pCR or be classified with RCB II/III.
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Affiliation(s)
- Qing Zhou
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Simon P. Gampenrieder
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research (LIMCR) and Center for Clinical Cancer and Immunology Trials (CCCIT), Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | - Sophie Frantal
- Department of Statistics, Austrian Breast and Colorectal Cancer Study Group, Vienna, Austria
| | - Gabriel Rinnerthaler
- IIIrd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research (LIMCR) and Center for Clinical Cancer and Immunology Trials (CCCIT), Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | - Christian F. Singer
- Department of Gynecology and Gynecological Oncology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Daniel Egle
- Department of Obstetrics and Gynecology, Medical University Innsbruck, Innsbruck, Austria
| | - Georg Pfeiler
- Department of Gynecology and Gynecological Oncology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Viktor Wette
- Breast Center, Brustzentrum Kaernten, St. Veit, Austria
| | - Angelika Pichler
- Department of Hemato-Oncology, LKH Hochsteiermark-Leoben, Leoben, Austria
| | - Edgar Petru
- Department of Gynaecology and Obstetrics, Medical University Graz, Graz, Austria
| | - Peter C. Dubsky
- Department of Surgery and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,Breast Center St. Anna, Lucerne, Switzerland
| | - Zsuzsanna Bago-Horvath
- Department of Surgery and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian Fesl
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research (LIMCR) and Center for Clinical Cancer and Immunology Trials (CCCIT), Salzburg, Austria
| | - Margaretha Rudas
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Anders Ståhlberg
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenberg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Ricarda Graf
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Sabrina Weber
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Nadia Dandachi
- Division of Oncology, Department of Internal Medicine, Medical University Graz, Graz, Austria
| | - Martin Filipits
- Department of Medicine I, Comprehensive Cancer Center, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University Graz, Graz, Austria.,Corresponding Authors: Ellen Heitzer, D&R Institute of Human Genetics, Medical University of Graz, Neue Stiftingtalstrasse 6, Graz, 8010, Austria. E-mail: ; and Marija Balic, Department of Internal Medicine, Division of Oncology, Medical University Graz, Auenbruggerplatz 15, 8010 Graz, Austria. E-mail:
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.,Corresponding Authors: Ellen Heitzer, D&R Institute of Human Genetics, Medical University of Graz, Neue Stiftingtalstrasse 6, Graz, 8010, Austria. E-mail: ; and Marija Balic, Department of Internal Medicine, Division of Oncology, Medical University Graz, Auenbruggerplatz 15, 8010 Graz, Austria. E-mail:
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10
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Suppan C, Graf R, Jahn S, Zhou Q, Klocker EV, Bartsch R, Terbuch A, Kashofer K, Regitnig P, Lindenmann J, Posch F, Gerritsmann H, Jost PJ, Heitzer E, Dandachi N, Balic M. Sensitive and robust liquid biopsy-based detection of PIK3CA mutations in hormone-receptor-positive metastatic breast cancer patients. Br J Cancer 2022; 126:456-463. [PMID: 34754095 PMCID: PMC8810831 DOI: 10.1038/s41416-021-01601-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The benefit of alpelisib in hormone-receptor-positive (HR+) metastatic breast cancer patients provided clinical evidence for the increasing importance of PIK3CA testing. We performed a comparison of liquid biopsy and tissue-based detection of PIK3CA mutations. MATERIALS AND METHODS PIK3CA hotspot mutation analysis using a high-resolution SiMSen-Seq assay was performed in plasma from 93/99 eligible patients with HR+/HER2- breast cancer. Additionally, mFAST-SeqS was used to estimate the tumour fractions in plasma samples. In 72/93 patients, matched tissue was available and analysed using a customised Ion Torrent panel. RESULTS PIK3CA mutations were detected in 48.6% of tissue samples and 47.3% of plasma samples, with identical PIK3CA mutation detected in 24/72 (33.3%) patients both in tissue and plasma. In 10 (13.9%) patients, mutations were only found in plasma, and in 6 (8.3%) patients, PIK3CA mutations found in tissue were not detectable in ctDNA. In 49/93 plasma samples without detectable PIK3CA mutations, 22 (44.9%) samples had elevated tumour fractions, implying true negative results. CONCLUSION SiMSen-Seq-based detection of PIK3CA mutations in plasma shows advantageous concordance with the tissue analyses. A combination with an untargeted approach for detecting ctDNA fractions may confirm a negative PIK3CA result and enhance the performance of the SiMSen-Seq test.
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Affiliation(s)
- Christoph Suppan
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Medical University of Graz, Graz, Austria
| | - Stephan Jahn
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Medical University of Graz, Graz, Austria
| | - Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Rupert Bartsch
- Department of Medicine 1, Clinical Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Angelika Terbuch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter Regitnig
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Joerg Lindenmann
- Division of Thoracic Surgery and Hyperbaric Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Florian Posch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | | | - Philipp J Jost
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine III, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Nadia Dandachi
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
- Research Unit Epigenetic and Genetic Cancer Biomarkers, Medical University of Graz, Graz, Austria.
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
- Research Unit Translational Breast Cancer, Medical University of Graz, Graz, Austria.
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11
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Wu Q, Zheng H, Gu J, Cheng Y, Qiao B, Wang J, Xiong L, Sun S, Wu Z, Bao A, Tong Y. Detection of folate receptor-positive circulating tumor cells as a biomarker for diagnosis, prognostication, and therapeutic monitoring in breast cancer. J Clin Lab Anal 2021; 36:e24180. [PMID: 34919735 PMCID: PMC8761444 DOI: 10.1002/jcla.24180] [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: 10/27/2021] [Revised: 11/14/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022] Open
Abstract
Objectives This study is to explore the clinical significance of folate receptor‐positive circulating tumor cells (FR+CTC) in the early diagnosis and disease progress in patients with breast cancer. Methods Folate receptor‐positive circulating tumor cells was enriched from peripheral blood of the patients with immunomagnetic separation method and quantitated by folate receptor on the CTC with the ligand‐targeted PCR. Results The levels of FR+CTC were significantly higher in breast cancer patients compared with healthy controls. Detective rate of FR+CTC was decreased in 19 of 27 patients underwent the surgery in 2 weeks post‐operation compared with pre‐operation; statistical analysis showed the difference was significant. We also found that the combination of FR+CTC, CEA, CA125, and CA153 can significantly improve the diagnostic efficiency for breast cancer. Conclusions This study showed the detective rate of FR+CTC is significantly increased in the patients with breast cancer, and the detective level is associated with disease progress.
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Affiliation(s)
- Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Hongyun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Yanfang Cheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Qiao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingwei Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Liang Xiong
- Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Si Sun
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zegang Wu
- Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
| | - Anyu Bao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Clinical Molecular Diagnostics Institute of Wuhan University, Wuhan, China
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12
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Bortolini Silveira A, Bidard FC, Tanguy ML, Girard E, Trédan O, Dubot C, Jacot W, Goncalves A, Debled M, Levy C, Ferrero JM, Jouannaud C, Rios M, Mouret-Reynier MA, Dalenc F, Hego C, Rampanou A, Albaud B, Baulande S, Berger F, Lemonnier J, Renault S, Desmoulins I, Proudhon C, Pierga JY. Multimodal liquid biopsy for early monitoring and outcome prediction of chemotherapy in metastatic breast cancer. NPJ Breast Cancer 2021; 7:115. [PMID: 34504096 PMCID: PMC8429692 DOI: 10.1038/s41523-021-00319-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are two cancer-derived blood biomarkers that inform on patient prognosis and treatment efficacy in breast cancer. We prospectively evaluated the clinical validity of quantifying both CTCs (CellSearch) and ctDNA (targeted next-generation sequencing). Their combined value as prognostic and early monitoring markers was assessed in 198 HER2-negative metastatic breast cancer patients. All patients were included in the prospective multicenter UCBG study COMET (NCT01745757) and treated by first-line chemotherapy with weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline and before the second cycle of chemotherapy. At baseline, CTCs and ctDNA were respectively detected in 72 and 74% of patients and were moderately correlated (Kendall’s τ = 0.3). Only 26 (13%) patients had neither detectable ctDNA nor CTCs. Variants were most frequently observed in TP53 and PIK3CA genes. KMT2C/MLL3 variants detected in ctDNA were significantly associated with a lower CTC count, while the opposite trend was seen with GATA3 alterations. Both CTC and ctDNA levels at baseline and after four weeks of treatment were correlated with survival. For progression-free and overall survival, the best multivariate prognostic model included tumor subtype (triple negative vs other), grade (grade 3 vs other), ctDNA variant allele frequency (VAF) at baseline (per 10% increase), and CTC count at four weeks (≥5CTC/7.5 mL). Overall, this study demonstrates that CTCs and ctDNA have nonoverlapping detection profiles and complementary prognostic values in metastatic breast cancer patients. A comprehensive liquid-biopsy approach may involve simultaneous detection of ctDNA and CTCs.
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Affiliation(s)
| | - François-Clément Bidard
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France.,UVSQ, Université Paris-Saclay, Paris, France
| | | | - Elodie Girard
- INSERM U900, Institut Curie, Mines ParisTech, PSL Research University, Paris, France
| | - Olivier Trédan
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Coraline Dubot
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France
| | - William Jacot
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier University, IRCM INSERM, Montpellier, France
| | - Anthony Goncalves
- Department of Medical Oncology, Aix-Marseille Univ, INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Marc Debled
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - Christelle Levy
- Department of Medical Oncology, Centre François Baclesse, Caen, France
| | - Jean-Marc Ferrero
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | | | - Maria Rios
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | | | - Florence Dalenc
- Department of Medical Oncology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Caroline Hego
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Benoit Albaud
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | | | | | - Shufang Renault
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Isabelle Desmoulins
- Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,INSERM U934 CNRS UMR3215, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France. .,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France. .,Université de Paris, Paris, France.
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13
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Dandachi N, Posch F, Graf R, Suppan C, Klocker EV, Müller HD, Lindenmann J, Terbuch A, Heitzer E, Balic M. Longitudinal tumor fraction trajectories predict risk of progression in metastatic HR + breast cancer patients undergoing CDK4/6 treatment. Mol Oncol 2021; 15:2390-2400. [PMID: 33264486 PMCID: PMC8410553 DOI: 10.1002/1878-0261.12870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Despite improved clinical outcomes, intrinsic or acquired resistance to CDK4/6 inhibitor treatment has limited the success of this treatment in HR+ HER2- metastatic breast cancer patients. Biomarkers are urgently needed, and longitudinal biomarker measurements may harbor more dynamic predictive and prognostic information compared to single time point measurements. The aim of this study was to explore the longitudinal evolution of circulating tumor fractions within cell-free DNA assessed by an untargeted sequencing approach during CDK4/6 therapy and to quantify the potential association between longitudinal z-score measurements and clinical outcome by using joint models. Forty-nine HR+ HER2- metastatic breast cancer patients were enrolled, and z-score levels were measured at baseline and during 132 follow-up visits (median number of measurements per patient = 3, 25th -75th percentile: 3-5, range: 1-8). We observed higher baseline z-score levels (estimated difference 0.57, 95% CI: 0.147-0.983, P-value = 0.008) and a constant increase of z-score levels over follow-up time (overall P-value for difference in log z-score over time = 0.024) in patients who developed progressive disease. Importantly, the joint model revealed that elevated z-score trajectories were significantly associated with higher progression risk (HR of log z-score at any time of follow-up = 3.3, 95% CI, 1.44-7.55, P = 0.005). In contrast, single z-score measurement at CDK4/6 inhibitor treatment start did not predict risk of progression. In this prospective study, we demonstrate proof-of-concept that longitudinal z-score trajectories rather than single time point measurements may harbor important dynamic information on the development of disease progression in HR+ HER2- breast cancer patients undergoing CDK4/6 inhibitor treatment.
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Affiliation(s)
- Nadia Dandachi
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
- Research Unit Epigenetic and Genetic Cancer BiomarkersMedical University of GrazAustria
| | - Florian Posch
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
| | - Ricarda Graf
- Institute of Human GeneticsDiagnostic and Research Center for Molecular BioMedicineChristian Doppler Laboratory for Liquid Biopsies for early Detection of CancerMedical University of GrazAustria
| | - Christoph Suppan
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
| | - Eva Valentina Klocker
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
| | - Hannah Deborah Müller
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
| | - Jörg Lindenmann
- Divison of Thoracic and Hyperbaric SurgeryDepartment of SurgeryMedical University of GrazAustria
| | - Angelika Terbuch
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
| | - Ellen Heitzer
- Institute of Human GeneticsDiagnostic and Research Center for Molecular BioMedicineChristian Doppler Laboratory for Liquid Biopsies for early Detection of CancerMedical University of GrazAustria
| | - Marija Balic
- Division of OncologyDepartment of Internal MedicineMedical University of GrazAustria
- Research Unit Circulating Tumor Cells and Cancer Stem CellsMedical University of GrazAustria
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14
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Yi Z, Ma F, Rong G, Liu B, Guan Y, Li J, Sun X, Wang W, Guan X, Mo H, Wang J, Qian H, Xu B. The molecular tumor burden index as a response evaluation criterion in breast cancer. Signal Transduct Target Ther 2021; 6:251. [PMID: 34230452 PMCID: PMC8260637 DOI: 10.1038/s41392-021-00662-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Circulating tumor DNA (ctDNA) is a potential biomarker of prognosis and therapeutic response. We conducted this study to explore the role of the molecular tumor burden index (mTBI) in ctDNA as a therapeutic response and prognostic biomarker in a larger cohort prospective phase III randomized multicenter study. We collected 291 plasma samples from 125 metastatic breast cancer patients from the CAMELLIA study (NCT01917279). Target-capture deep sequencing of 1021 genes was performed to detect somatic variants in ctDNA from the plasma samples. The pretreatment mTBI value was correlated with tumor burden (P = 0.025). Patients with high-level pretreatment mTBI had shorter overall survival than patients with low-level pretreatment mTBI, and the median overall survival was 40.9 months and 68.4 months, respectively (P = 0.011). Patients with mTBI decrease to less than 0.02% at the first tumor evaluation had longer progression-free survival and overall survival (P < 0.001 and P = 0.007, respectively). The mTBI has good sensitivity to identify complete response/partial response and progressive disease based on computed tomography scans (88.5% and 87.5%, respectively). The patients classified as molecular responders had longer progression-free survival and overall survival than the nonmolecular responders in the overall cohort (P < 0.001 and P = 0.036, respectively), as well as in the cohort in which computed tomography scans were defined as representing stable disease (P = 0.027 and P = 0.015, respectively). The mTBI in ctDNA detected in liquid biopsies is a potential biomarker of therapeutic response and prognosis in patients with metastatic breast cancer.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Guohua Rong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Jin Li
- Geneplus-Beijing Institute, Beijing, China
| | - Xiaoying Sun
- Department of Medical Oncology, Huanxing Cancer Hospital, Beijing, China
| | - Wenna Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongnan Mo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiani Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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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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16
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Drug Resistance and Novel Therapies in Cancers in 2019. Cancers (Basel) 2021; 13:cancers13040924. [PMID: 33672119 PMCID: PMC7926476 DOI: 10.3390/cancers13040924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
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17
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Angus L, Deger T, Jager A, Martens JWM, de Weerd V, van Heuvel I, van den Bent MJ, Sillevis Smitt PAE, Kros JM, Bindels EMJ, Heitzer E, Sleijfer S, Jongen JLM, Wilting SM. Detection of Aneuploidy in Cerebrospinal Fluid from Patients with Breast Cancer Can Improve Diagnosis of Leptomeningeal Metastases. Clin Cancer Res 2021; 27:2798-2806. [PMID: 33514525 DOI: 10.1158/1078-0432.ccr-20-3954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Detection of leptomeningeal metastasis is hampered by limited sensitivities of currently used techniques: MRI and cytology of cerebrospinal fluid (CSF). Detection of cell-free tumor DNA in CSF has been proposed as a tumor-specific candidate to detect leptomeningeal metastasis at an earlier stage. The aim of this study was to investigate mutation and aneuploidy status in CSF-derived cell-free DNA (cfDNA) of patients with breast cancer with a clinical suspicion of leptomeningeal metastasis. EXPERIMENTAL DESIGN cfDNA was isolated from stored remnant CSF and analyzed by targeted next-generation sequencing (NGS; n = 30) and the modified fast aneuploidy screening test-sequencing system (mFAST-SeqS; n = 121). The latter method employs selective amplification of long interspaced nuclear elements sequences that are present throughout the genome and allow for fast and cheap detection of aneuploidy. We compared these results with the gold standard to diagnose leptomeningeal metastasis: cytology. RESULTS Leptomeningeal metastasis was cytology proven in 13 of 121 patients. Low DNA yields resulted in insufficient molecular coverage of NGS for the majority of samples (success rate, 8/30). The mFAST-SeqS method, successful in 112 of 121 (93%) samples, detected genome-wide aneuploidy in 24 patients. Ten of these patients had cytology-proven leptomeningeal metastasis; 8 additional patients were either concurrently diagnosed with central nervous system metastases by radiological means or developed these soon after the lumbar puncture. The remaining six cases were suspected of leptomeningeal metastasis, but could not be confirmed by cytology or imaging. Aneuploidy was associated with development of leptomeningeal metastasis and significantly worse overall survival. CONCLUSIONS Aneuploidy in CSF-derived cfDNA may provide a promising biomarker to improve timely detection of leptomeningeal metastasis.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, 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
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Irene van Heuvel
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin J van den Bent
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter A E Sillevis Smitt
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Eric M J Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ellen Heitzer
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joost L M Jongen
- Department of Neurology, The Brain Tumor Center at 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
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18
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Unseld M, Belic J, Pierer K, Zhou Q, Moser T, Bauer R, Piringer G, Gerger A, Siebenhüner A, Speicher M, Heitzer E, Prager GW. A higher ctDNA fraction decreases survival in regorafenib-treated metastatic colorectal cancer patients. Results from the regorafenib's liquid biopsy translational biomarker phase II pilot study. Int J Cancer 2020; 148:1452-1461. [PMID: 32949150 PMCID: PMC7894541 DOI: 10.1002/ijc.33303] [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: 06/12/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022]
Abstract
The predictive effect of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) treatment is still highly discussed. The primary objective of our study was to investigate a possible prognostic/predictive value of ctDNA under regorafenib treatment. This prospective multicenter translational biomarker phase II pilot study enrolled 30 metastatic CRC patients (67% men, 33% women) treated with regorafenib. ctDNA was assessed in plasma before treatment start and at defined time points during administration. Measurement of tumor fraction as well as mutation and copy number analysis of CRC driver genes were performed by next-generation sequencing approaches. Multivariate analyses for survival and treatment efficacy were adjusted to age, gender and Eastern Cooperative Oncology Group. Disease control rate was 30%. Median tumor fraction at baseline was 18.5% (0-49.9). Mutations in CRC driver genes or genes involved in angiogenesis were identified in 25 patients (83.3%). KRAS mutations were detected in 13 of 14 KRAS-positive tumors; in three patients without KRAS mutation in the respective tumors, acquired mutations as a consequence of prior anti-EGFR treatment were detected. In a subset of patients, novel occurring mutations or focal amplifications were detected. A tumor fraction of 5% and higher at baseline was significantly associated with a decreased OS (P = .022; hazard ratio 3.110 (95% confidence interval: 1.2-8.2). ctDNA is detectable in a high proportion of mCRC patients. Higher ctDNA levels are associated with survival among regorafenib treatment. Moreover, our data highlight the benefit of a combined evaluation of mutations and somatic copy number alterations in advanced cancer patients.
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Affiliation(s)
- Matthias Unseld
- Department of Medicine I, Division of Palliative Medicine, Medical University of Vienna, Vienna, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Kerstin Pierer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Raimund Bauer
- Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | | | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Austria
| | | | - Michael Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Gerald W Prager
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
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Bourrier C, Pierga JY, Xuereb L, Salaun H, Proudhon C, Speicher MR, Belic J, Heitzer E, Lockhart BP, Guigal-Stephan N. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers (Basel) 2020; 12:cancers12061481. [PMID: 32517171 PMCID: PMC7353062 DOI: 10.3390/cancers12061481] [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: 04/14/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open
Abstract
Background: Focal amplification of fibroblast growth factor receptor 1 (FGFR1) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (OncoscanTM). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% (n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials.
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Affiliation(s)
- Chantal Bourrier
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.)
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France;
- Université de Paris, 75005 Paris, France
| | - Laura Xuereb
- Division of Methodology and Valorisation of Data, Servier Research and Development Institute, 50 rue carnot, 92150 Suresnes, France;
| | - Hélène Salaun
- Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.)
- Université de Paris, 75005 Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France;
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
- BioTechMed-Graz, 8010 Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
- BioTechMed-Graz, 8010 Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8010 Graz, Austria
| | - Brian Paul Lockhart
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
| | - Nolwen Guigal-Stephan
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
- Correspondence: ; Tel.: +33-155-722-532
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20
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van der Leest P, Schuuring E. The potential of combined mutation sequencing of plasma circulating cell-free DNA and matched white blood cells for treatment response prediction. Mol Oncol 2020; 14:487-489. [PMID: 32017376 PMCID: PMC7053232 DOI: 10.1002/1878-0261.12646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/14/2023] Open
Abstract
Highly sensitive mutation detection methods enable the application of circulating cell-free DNA for molecular tumor profiling. Recent studies revealed that sequencing artifacts, germline variants, and clonal hematopoiesis confound the interpretation of sequencing results and complicate subsequent treatment decision making and disease monitoring. Parallel sequencing of matched white blood cells promises to overcome these issues and enables appropriate variant calling. Comment on: https://doi.org/10.1002/1878-0261.12617.
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Affiliation(s)
- Paul van der Leest
- Laboratory of Molecular PathologyDepartment of Pathology (EA10)University Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Ed Schuuring
- Laboratory of Molecular PathologyDepartment of Pathology (EA10)University Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
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21
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Smith CG, Moser T, Mouliere F, Field-Rayner J, Eldridge M, Riediger AL, Chandrananda D, Heider K, Wan JCM, Warren AY, Morris J, Hudecova I, Cooper WN, Mitchell TJ, Gale D, Ruiz-Valdepenas A, Klatte T, Ursprung S, Sala E, Riddick ACP, Aho TF, Armitage JN, Perakis S, Pichler M, Seles M, Wcislo G, Welsh SJ, Matakidou A, Eisen T, Massie CE, Rosenfeld N, Heitzer E, Stewart GD. Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors. Genome Med 2020; 12:23. [PMID: 32111235 PMCID: PMC7048087 DOI: 10.1186/s13073-020-00723-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established. METHODS Here, a combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n = 91) with various renal tumor subtypes, were used to determine ctDNA content in plasma and urine. RESULTS Our data revealed lower plasma ctDNA levels in RCC relative to other cancers of similar size and stage, with untargeted detection in 27.5% of patients from both cohorts. A sensitive personalized approach, applied to plasma and urine from select patients (n = 22) improved detection to ~ 50%, including in patients with early-stage disease and even benign lesions. Detection in plasma, but not urine, was more frequent amongst patients with larger tumors and in those patients with venous tumor thrombus. With data from one extensively characterized patient, we observed that plasma and, for the first time, urine ctDNA may better represent tumor heterogeneity than a single tissue biopsy. Furthermore, in a subset of patients (n = 16), longitudinal sampling revealed that ctDNA can track disease course and may pre-empt radiological identification of minimal residual disease or disease progression on systemic therapy. Additional datasets will be required to validate these findings. CONCLUSIONS These data highlight RCC as a ctDNA-low malignancy. The biological reasons for this are yet to be determined. Nonetheless, our findings indicate potential clinical utility in the management of patients with renal tumors, provided improvement in isolation and detection approaches.
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Affiliation(s)
- Christopher G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Tina Moser
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Florent Mouliere
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - Johanna Field-Rayner
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anja L Riediger
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Irena Hudecova
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andrea Ruiz-Valdepenas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tobias Klatte
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Urology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Stephan Ursprung
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Evis Sala
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Antony C P Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Tevita F Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Samantha Perakis
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine Graz, Austria Division of Oncology, Medical University of Graz, Graz, Austria
| | - Maximilian Seles
- Department of Urology, Medical University of Graz, Graz, Austria
| | - Gabriel Wcislo
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Sarah J Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Athena Matakidou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Charles E Massie
- Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ellen Heitzer
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Grant D Stewart
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
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