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Lianidou E, Pantel K. Liquid biopsies. Genes Chromosomes Cancer 2019; 58:219-232. [PMID: 30382599 DOI: 10.1002/gcc.22695] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/28/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is based on minimally invasive blood tests and has a high potential to significantly change the therapeutic strategy in cancer patients, providing an extremely powerful and reliable noninvasive clinical tool for the individual molecular profiling of patients in real time. Liquid biopsy approaches include the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs) that are shed from primary tumors and their metastatic sites into peripheral blood. The major advantage of liquid biopsy analysis is that it is minimally invasive, and can be serially repeated, thus allowing extracting information from the tumor in real time. Moreover, the identification of predictive biomarkers in peripheral blood that can monitor response to therapy in real time holds a very strong potential for novel approaches in the therapeutic management of cancer patients. In this review, we summarize recent knowledge on CTCs and ctDNA and discuss future trends in the field.
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Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Department of Chemistry, University of Athens, Athens, Greece
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Paolillo C, Londin E, Fortina P. Single-Cell Genomics. Clin Chem 2019; 65:972-985. [PMID: 30872376 DOI: 10.1373/clinchem.2017.283895] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Single-cell genomics is an approach to investigate cell heterogeneity and to identify new molecular features correlated with clinical outcomes. This approach allows identification of the complexity of cell diversity in a sample without the loss of information that occurs when multicellular or bulk tissue samples are analyzed. CONTENT The first single-cell RNA-sequencing study was published in 2009, and since then many more studies and single-cell sequencing methods have been published. These studies have had a major impact on several fields, including microbiology, neurobiology, cancer, and developmental biology. Recently, improvements in reliability and the development of commercial single-cell isolation platforms are opening the potential of this technology to the clinical laboratory. SUMMARY In this review we provide an overview of the current state of single-cell genomics. We describe opportunities in clinical research and medical applications.
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Affiliation(s)
- Carmela Paolillo
- Division of Precision and Computational Diagnostics, Department of Clinical Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Paolo Fortina
- Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA; .,Department of Molecular Medicine, Sapienza University, Rome, Italy
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53
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Cariati F, Borrillo F, Shankar V, Nunziato M, D'Argenio V, Tomaiuolo R. Dissecting Intra-Tumor Heterogeneity by the Analysis of Copy Number Variations in Single Cells: The Neuroblastoma Case Study. Int J Mol Sci 2019; 20:ijms20040893. [PMID: 30791380 PMCID: PMC6412524 DOI: 10.3390/ijms20040893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/11/2019] [Accepted: 02/15/2019] [Indexed: 02/07/2023] Open
Abstract
Tumors often show intra-tumor heterogeneity because of genotypic differences between all the cells that compose it and that derive from it. Recent studies have shown significant aspects of neuroblastoma heterogeneity that may affect the diagnostic-therapeutic strategy. Therefore, we developed a laboratory protocol, based on the combination of the advanced dielectrophoresis-based array technology and next-generation sequencing to identify and sort single cells individually and carry out their copy number variants analysis. The aim was to evaluate the cellular heterogeneity, avoiding overestimation or underestimation errors, due to a bulk analysis of the sample. We tested the above-mentioned protocol on two neuroblastoma cell lines, SK-N-BE(2)-C and IMR-32. The presence of several gain or loss chromosomal regions, in both cell lines, shows a high heterogeneity of the copy number variants status of the single tumor cells, even if they belong to an immortalized cell line. This finding confirms that each cell can potentially accumulate different alterations that can modulate its behavior. The laboratory protocol proposed herein provides a tool able to identify prevalent behaviors, and at the same time highlights the presence of particular clusters that deviate from them. Finally, it could be applicable to many other types of cancer.
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Affiliation(s)
- Federica Cariati
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Francesca Borrillo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
| | - Varun Shankar
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Marcella Nunziato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
| | - Valeria D'Argenio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Rossella Tomaiuolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
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Keup C, Storbeck M, Hauch S, Hahn P, Sprenger-Haussels M, Tewes M, Mach P, Hoffmann O, Kimmig R, Kasimir-Bauer S. Cell-Free DNA Variant Sequencing Using CTC-Depleted Blood for Comprehensive Liquid Biopsy Testing in Metastatic Breast Cancer. Cancers (Basel) 2019; 11:E238. [PMID: 30781720 PMCID: PMC6406821 DOI: 10.3390/cancers11020238] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy analytes such as cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for personalized treatment. Since cfDNA and CTCs are considered to give additive information and blood specimens are limited, isolation of cfDNA and CTC in an "all from one tube" format is desired. We investigated whether cfDNA variant sequencing from CTC-depleted blood (CTC-depl. B; obtained after positive immunomagnetic isolation of CTCs (AdnaTest EMT-2/Stem Cell Select, QIAGEN)) impacts the results compared to cfDNA variant sequencing from matched whole blood (WB). Cell-free DNA was isolated using matched WB and CTC-depl. B from 17 hormone receptor positive/human epidermal growth factor receptor 2 negative (HR+/HER2-) metastatic breast cancer patients (QIAamp MinElute ccfDNA Kit, QIAGEN). Cell-free DNA libraries were constructed (customized QIAseq Targeted DNA Panel for Illumina, QIAGEN) with integrated unique molecular indices. Sequencing (on the NextSeq 550 platform, Illumina) and data analysis (Ingenuity Variant Analysis) were performed. RNA expression in CTCs was analyzed by multimarker quantitative PCR. Cell-free DNA concentration and size distribution in the matched plasma samples were not significantly different. Seventy percent of all variants were identical in matched WB and CTC-depl. B, but 115/125 variants were exclusively found in WB/CTC-depl. B. The number of detected variants per patient and the number of exclusively detected variants per patient in only one cfDNA source did not differ between the two matched cfDNA sources. Even the characteristics of the exclusively detected cfDNA variants in either WB or CTC-depl. B were comparable. Thus, cfDNA variants from matched WB and CTC-depl. B exhibited no relevant differences, and parallel isolation of cfDNA and CTCs from only 10 mL of blood in an "all from one tube" format was feasible. Matched cfDNA mutational and CTC transcriptional analyses might empower a comprehensive liquid biopsy analysis to enhance the identification of actionable targets for individual therapy strategies.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany.
| | | | | | | | | | - Mitra Tewes
- Department of Medical Oncology, University Hospital of Essen, 45122 Essen, Germany.
| | - Pawel Mach
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany.
| | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany.
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany.
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany.
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Pallante P, Pisapia P, Bellevicine C, Malapelle U, Troncone G. Circulating Tumour Cells in Predictive Molecular Pathology: Focus on Drug-Sensitive Assays and 3D Culture. Acta Cytol 2019; 63:171-181. [PMID: 30759433 DOI: 10.1159/000496213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/13/2018] [Indexed: 12/19/2022]
Abstract
Molecular cytopathology is a rapidly evolving field of cytopathology that provides biological information about the response to personalised therapy and about the prognosis of neoplasms diagnosed on cytological samples. Biomarkers such as circulating tumour cells and circulating tumour DNA are increasingly being evaluated in blood and in other body fluids. Such liquid biopsies are non-invasive, repeatable, and feasible also in patients with severe comorbidities. However, liquid biopsy may be challenging due to a low concentration of biomarkers. In such cases, biomarkers can be detected with highly sensitive molecular techniques, which in turn should be validated and integrated in a complex algorithm that includes tissue-based molecular assessments. The aim of this review is to provide the cytopathologist with practical information that is relevant to daily practice, particularly regarding the emerging role of circulating tumour cells in the field of predictive molecular pathology.
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Affiliation(s)
- Pierlorenzo Pallante
- Institute of Experimental Endocrinology and Oncology (IEOS) "G. Salvatore," National Research Council (CNR), Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy,
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Cristofanilli M, Pierga JY, Reuben J, Rademaker A, Davis AA, Peeters DJ, Fehm T, Nolé F, Gisbert-Criado R, Mavroudis D, Grisanti S, Giuliano M, Garcia-Saenz JA, Stebbing J, Caldas C, Gazzaniga P, Manso L, Zamarchi R, de Lascoiti AF, De Mattos-Arruda L, Ignatiadis M, Cabel L, van Laere SJ, Meier-Stiegen F, Sandri MT, Vidal-Martinez J, Politaki E, Consoli F, Generali D, Cappelletti MR, Diaz-Rubio E, Krell J, Dawson SJ, Raimondi C, Rutten A, Janni W, Munzone E, Carañana V, Agelaki S, Almici C, Dirix L, Solomayer EF, Zorzino L, Darrigues L, Reis-Filho JS, Gerratana L, Michiels S, Bidard FC, Pantel K. The clinical use of circulating tumor cells (CTCs) enumeration for staging of metastatic breast cancer (MBC): International expert consensus paper. Crit Rev Oncol Hematol 2019; 134:39-45. [PMID: 30771872 DOI: 10.1016/j.critrevonc.2018.12.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The heterogeneity of metastatic breast cancer (MBC) necessitates novel biomarkers allowing stratification of patients for treatment selection and drug development. We propose to use the prognostic utility of circulating tumor cells (CTCs) for stratification of patients with stage IV disease. METHODS In a retrospective, pooled analysis of individual patient data from 18 cohorts, including 2436 MBC patients, a CTC threshold of 5 cells per 7.5 ml was used for stratification based on molecular subtypes, disease location, and prior treatments. Patients with ≥ 5 CTCs were classified as Stage IVaggressive, those with < 5 CTCs as Stage IVindolent. Survival was analyzed using Kaplan-Meier curves and the log rank test. RESULTS For all patients, Stage IVindolent patients had longer median overall survival than those with Stage IVaggressive (36.3 months vs. 16.0 months, P < 0.0001) and similarly for de novo MBC patients (41.4 months Stage IVindolent vs. 18.7 months Stage IVaggressive, p < 0.0001). Moreover, patients with Stage IVindolent disease had significantly longer overall survival across all disease subtypes compared to the aggressive cohort: hormone receptor-positive (44 months vs. 17.3 months, P < 0.0001), HER2-positive (36.7 months vs. 20.4 months, P < 0.0001), and triple negative (23.8 months vs. 9.0 months, P < 0.0001). Similar results were obtained regardless of prior treatment or disease location. CONCLUSIONS We confirm the identification of two subgroups of MBC, Stage IVindolent and Stage IVaggressive, independent of clinical and molecular variables. Thus, CTC count should be considered an important tool for staging of advanced disease and for disease stratification in prospective clinical trials.
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Affiliation(s)
- Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - James Reuben
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alfred Rademaker
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Andrew A Davis
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dieter J Peeters
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | - Tanja Fehm
- Department of Gynecology and Obstetrics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Franco Nolé
- Division of Medical Senology, European Institute of Oncology, Milan, Italy
| | | | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Greece; Department of Medical Oncology, University Hospital of Heraklion, Greece
| | - Salvatore Grisanti
- Department of Transfusion Medicine, Laboratory for Stem Cells Manipulation and Cryopreservation, AO Spedali Civili di Brescia, Brescia, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
| | | | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Paola Gazzaniga
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Rita Zamarchi
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Leticia De Mattos-Arruda
- Val d'Hebron Institute of Oncology, Val d'Hebron University Hospital, and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Michail Ignatiadis
- Department of Medical Oncology and Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Steven J van Laere
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | - Franziska Meier-Stiegen
- Department of Gynecology and Obstetrics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maria-Teresa Sandri
- Division of Laboratory Medicine, Humanitas Reseach Hospital, Rozzano, Milan, Italy
| | | | - Eleni Politaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Greece; Department of Medical Oncology, University Hospital of Heraklion, Greece
| | - Francesca Consoli
- Department of Transfusion Medicine, Laboratory for Stem Cells Manipulation and Cryopreservation, AO Spedali Civili di Brescia, Brescia, Italy
| | - Daniele Generali
- Women Cancer Center, Azienda Socio Sanitaria Territoriale di Cremona, University of Trieste, Italy
| | - Maria Rosa Cappelletti
- Women Cancer Center, Azienda Socio Sanitaria Territoriale di Cremona, University of Trieste, Italy
| | | | - Jonathan Krell
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Cristina Raimondi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annemie Rutten
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | | | - Elisabetta Munzone
- Division of Medical Senology, European Institute of Oncology, Milan, Italy
| | | | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Greece; Department of Medical Oncology, University Hospital of Heraklion, Greece
| | - Camillo Almici
- Department of Transfusion Medicine, Laboratory for Stem Cells Manipulation and Cryopreservation, AO Spedali Civili di Brescia, Brescia, Italy
| | - Luc Dirix
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium
| | | | - Laura Zorzino
- Division of Laboratory Medicine, Humanitas Reseach Hospital, Rozzano, Milan, Italy
| | - Lauren Darrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Gerratana
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Medicine, University of Udine, Udine, UD, Italy
| | - Stefan Michiels
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, CESP, INSERM U1018, University Paris-Saclay, University Paris-Sud, Villejuif, France
| | | | - Klaus Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Buono G, Gerratana L, Bulfoni M, Provinciali N, Basile D, Giuliano M, Corvaja C, Arpino G, Del Mastro L, De Placido S, De Laurentiis M, Cristofanilli M, Puglisi F. Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? Cancer Treat Rev 2019; 73:73-83. [PMID: 30682661 DOI: 10.1016/j.ctrv.2019.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
Abstract
Precision Medicine is becoming the new paradigm in healthcare as it enables better resources allocation, treatment optimization with a potential side-effects reduction and consequent impact on quality of life and survival. This revolution is being catalyzed by liquid biopsy technologies, which provide prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue-biopsy. In particular, circulating tumor DNA (ctDNA) is gaining momentum as a clinically feasible option capable to capture both spatial and temporal tumor heterogeneity. Several techniques are currently available for ctDNA extraction and analysis, each with its preferential case scenarios and preanalytical implications which must be taken into consideration to effectively support clinical decision-making and to better highlight its clinical utility. Aim of this review is to summarize both analytical developments and clinical evidences to offer a comprehensive update on the deployment of ctDNA in breast cancer's (BC) characterization and treatment.
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Affiliation(s)
- Giuseppe Buono
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Italy; Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michela Bulfoni
- Department of Pathology, ASUIUD University Hospital, Udine, Italy
| | | | - Debora Basile
- Department of Medicine (DAME), University of Udine, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy; Lester and Sue Smith Breast Center at Baylor College of Medicine, Houston, TX, USA
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Italy
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lucia Del Mastro
- Department of Medical Oncology, IRCCS AOU San Martino-IST, National Cancer Institute, Genova, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, PN, Italy
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58
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Paoletti C, Cani AK, Larios JM, Hovelson DH, Aung K, Darga EP, Cannell EM, Baratta PJ, Liu CJ, Chu D, Yazdani M, Blevins AR, Sero V, Tokudome N, Thomas DG, Gersch C, Schott AF, Wu YM, Lonigro R, Robinson DR, Chinnaiyan AM, Bischoff FZ, Johnson MD, Park BH, Hayes DF, Rae JM, Tomlins SA. Comprehensive Mutation and Copy Number Profiling in Archived Circulating Breast Cancer Tumor Cells Documents Heterogeneous Resistance Mechanisms. Cancer Res 2018; 78:1110-1122. [PMID: 29233927 PMCID: PMC5815882 DOI: 10.1158/0008-5472.can-17-2686] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/19/2017] [Accepted: 12/07/2017] [Indexed: 01/05/2023]
Abstract
Addressing drug resistance is a core challenge in cancer research, but the degree of heterogeneity in resistance mechanisms in cancer is unclear. In this study, we conducted next-generation sequencing (NGS) of circulating tumor cells (CTC) from patients with advanced cancer to assess mechanisms of resistance to targeted therapy and reveal opportunities for precision medicine. Comparison of the genomic landscapes of CTCs and tissue metastases is complicated by challenges in comprehensive CTC genomic profiling and paired tissue acquisition, particularly in patients who progress after targeted therapy. Thus, we assessed by NGS somatic mutations and copy number alterations (CNA) in archived CTCs isolated from patients with metastatic breast cancer who were enrolled in concurrent clinical trials that collected and analyzed CTCs and metastatic tissues. In 76 individual and pooled informative CTCs from 12 patients, we observed 85% concordance in at least one or more prioritized somatic mutations and CNA between paired CTCs and tissue metastases. Potentially actionable genomic alterations were identified in tissue but not CTCs, and vice versa. CTC profiling identified diverse intra- and interpatient molecular mechanisms of endocrine therapy resistance, including loss of heterozygosity in individual CTCs. For example, in one patient, we observed CTCs that were either wild type for ESR1 (n = 5/32), harbored the known activating ESR1 p.Y537S mutation (n = 26/32), or harbored a novel ESR1 p.A569S (n = 1/32). ESR1 p.A569S was modestly activating in vitro, consistent with its presence as a minority circulating subclone. Our results demonstrate the feasibility and potential clinical utility of comprehensive profiling of archived fixed CTCs. Tissue and CTC genomic assessment are complementary, and precise combination therapies will likely be required for effective targeting in advanced breast cancer patients.Significance: These findings demonstrate the complementary nature of genomic profiling from paired tissue metastasis and circulating tumor cells from patients with metastatic breast cancer. Cancer Res; 78(4); 1110-22. ©2017 AACR.
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Affiliation(s)
- Costanza Paoletti
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Andi K Cani
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jose M Larios
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Daniel H Hovelson
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kimberly Aung
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Elizabeth P Darga
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Emily M Cannell
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Paul J Baratta
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine Department of Oncology, Baltimore, Maryland
| | - Maryam Yazdani
- Menarini Silicon Biosystems, Inc., San Diego, California
| | | | - Valeria Sero
- Menarini Silicon Biosystems, Inc., San Diego, California
| | - Nahomi Tokudome
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Present address: Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Dafydd G Thomas
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christina Gersch
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Anne F Schott
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Yi-Mi Wu
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Robert Lonigro
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Dan R Robinson
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Arul M Chinnaiyan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | | | | | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine Department of Oncology, Baltimore, Maryland
| | - Daniel F Hayes
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - James M Rae
- Breast Oncology Program of the University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Scott A Tomlins
- Comphrehensive Cancer Center, University of Michigan, Ann Arbor, Michigan.
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan
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59
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Li Y, Wu S, Bai F. Molecular characterization of circulating tumor cells-from bench to bedside. Semin Cell Dev Biol 2017; 75:88-97. [PMID: 28899718 DOI: 10.1016/j.semcdb.2017.09.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023]
Abstract
Circulating tumor cells (CTCs) are cancer cells discovered in cancer patients' peripheral blood that successfully escape from the primary tumor site and/or metastases, struggle to survive in the bloodstream, and have potential for seeding metastases. Numerous methods have been proposed to capture CTCs. The value of CTCs as a means of understanding cancer metastasis and a major form of 'liquid biopsy' has been widely demonstrated. Recently, single-cell molecular analyses of CTCs have provided profound biological insights into tumor heterogeneity, mechanism of metastasis and tumor evolution. In addition, because CTC analysis is non-invasive, CTCs exhibit great potential as biomarkers for assessment of cancer prognosis and therapy response. In this review, we summarize modern technologies for CTC detection and isolation, single-cell genomic/transcriptomic characterization of CTCs, and prospective clinical applications of CTCs. We expect that, after further technical improvements in methods of detection and sequencing, CTC analyses will shed new light on the mechanisms driving cancer metastasis and benefit many cancer patients.
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Affiliation(s)
- Yanmeng Li
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Science, Peking University, Beijing 100871, China
| | - Shaohan Wu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Science, Peking University, Beijing 100871, China
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Science, Peking University, Beijing 100871, China.
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