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Kindt CK, Alves CL, Ehmsen S, Kragh A, Reinert T, Vogsen M, Kodahl AR, Rønlev JD, Ardik D, Sørensen AL, Evald K, Clemmensen ML, Staaf J, Ditzel HJ. Genomic alterations associated with resistance and circulating tumor DNA dynamics for early detection of progression on CDK4/6 inhibitor in advanced breast cancer. Int J Cancer 2024. [PMID: 39128978 DOI: 10.1002/ijc.35126] [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: 01/22/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
Combined CDK4/6 inhibitor (CDK4/6i) and endocrine therapy significantly improves outcome for patients with estrogen receptor-positive (ER+) metastatic breast cancer, but drug resistance and thus disease progression inevitably occur. Herein, we aimed to identify genomic alterations associated with combined CDK4/6i and endocrine therapy resistance, and follow the levels of specific mutations in longitudinal circulating tumor DNA (ctDNA) for early detection of progression. From a cohort of 86 patients with ER+ metastatic breast cancer we performed whole exome sequencing or targeted sequencing of paired tumor (N = 8) or blood samples (N = 5) obtained before initiation of combined CDK4/6i and endocrine therapy and at disease progression. Mutations in oncogenic genes at progression were rare, while amplifications of growth-regulating genes were more frequent. The most frequently acquired alterations observed were PIK3CA and TP53 mutations and PDK1 amplification. Longitudinal ctDNA dynamics of mutant PIK3CA or private mutations revealed increased mutation levels at progression in 8 of 10 patients (80%). Impressively, rising levels of PIK3CA-mutated ctDNA were detected 4-17 months before imaging. Our data add to the growing evidence supporting longitudinal ctDNA analysis for real-time monitoring of CDK4/6i response and early detection of progression in advanced breast cancer. Further, our analysis suggests that amplification of growth-related genes may contribute to combined CDK4/6i and endocrine therapy resistance.
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Affiliation(s)
- Charlotte K Kindt
- Department of Cancer Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Carla L Alves
- Department of Cancer Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Sidse Ehmsen
- Department of Cancer Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Amalie Kragh
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Marianne Vogsen
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Annette R Kodahl
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jeanette D Rønlev
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Henrik J Ditzel
- Department of Cancer Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital; Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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2
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Afzal MZ, Vahdat LT. Evolving Management of Breast Cancer in the Era of Predictive Biomarkers and Precision Medicine. J Pers Med 2024; 14:719. [PMID: 39063972 PMCID: PMC11278458 DOI: 10.3390/jpm14070719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer is the most common cancer among women in the world as well as in the United States. Molecular and histological differentiation have helped clinicians optimize treatments with various therapeutics, including hormonal therapy, chemotherapy, immunotherapy, and radiation therapy. Recently, immunotherapy has become the standard of care in locally advanced triple-negative breast cancer and an option across molecular subtypes for tumors with a high tumor mutation burden. Despite the advancements in personalized medicine directing the management of localized and advanced breast cancers, the emergence of resistance to these therapies is the leading cause of death among breast cancer patients. Therefore, there is a critical need to identify and validate predictive biomarkers to direct treatment selection, identify potential responders, and detect emerging resistance to standard therapies. Areas of active scientific and clinical research include novel personalized and predictive biomarkers incorporating tumor microenvironment, tumor immune profiling, molecular characterization, and histopathological differentiation to predict response and the potential emergence of resistance.
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Affiliation(s)
- Muhammad Zubair Afzal
- Medical Oncology, Comprehensive Breast Program, Dartmouth Cancer Center, Lebanon, NH 03755, USA
| | - Linda T. Vahdat
- Medical Oncology and Hematology (Interim), Dartmouth Cancer Center, Lebanon, NH 03755, USA;
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3
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Najafi S, Asemani Y, Majidpoor J, Mahmoudi R, Aghaei-Zarch SM, Mortezaee K. Tumor-educated platelets. Clin Chim Acta 2024; 552:117690. [PMID: 38056548 DOI: 10.1016/j.cca.2023.117690] [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: 10/15/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/08/2023]
Abstract
Beyond traditional roles in homeostasis and coagulation, growing evidence suggests that platelets also reflect malignant transformation in cancer. Platelets are present in the tumor microenvironment where they interact with cancer cells. This interaction results in direct and indirect "education" as evident by platelet alterations in adhesion molecules, glycoproteins, nucleic acids, proteins and various receptors. Subsequently, these tumor-educated platelets (TEPs) circulate throughout the body and play pivotal roles in promotion of tumor growth and dissemination. Accordingly, platelet status can be considered a unique blood-based biomarker that can potentially predict prognosis and therapeutic success. Recently, liquid biopsies including TEPs have received much attention as safe, minimally invasive and sensitive alternatives for patient management. Herein, we provide an overview of TEPs and explore their benefits and limitations in cancer.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yahya Asemani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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4
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Allsopp RC, Page K, Ambasager B, Wadsley MK, Acheampong E, Ntereke TP, Guo Q, Lall GM, Gleason KLT, Wren E, Nteliopoulos G, Rushton AJ, Coombes RC, Shaw JA. A Rapid, Shallow Whole Genome Sequencing Workflow Applicable to Limiting Amounts of Cell-Free DNA. Clin Chem 2023; 69:510-518. [PMID: 36747279 DOI: 10.1093/clinchem/hvac220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Somatic copy number alterations (sCNAs) acquired during the evolution of breast cancer provide valuable prognostic and therapeutic information. Here we present a workflow for screening sCNAs using picogram amounts of cell-free DNA (cfDNA) and single circulating tumor cells (CTCs). METHODS We repurposed the Ion ReproSeq PGS™ preimplantation genetic testing kit to perform shallow whole genome sequencing on 178 cfDNA samples (300 pg) and individual CTCs from 10 MBC patients with metastatic breast cancer (MBC) recovered by CellSearch®/DEPArray™. Results were analyzed using a tailored ichorCNA workflow. RESULTS sCNAs were detected in cfDNA of 41/105 (39%) patients with MBC and 3/23 (13%) primary breast cancers on follow-up (PBC FU), all of whom subsequently relapsed. In 8 of 10 MBCs, individual CTCs had a higher copy number count than matched cfDNA. The median tumor fraction detected by ichorCNA was 0.34 (range 0.17-0.58) for MBC and 0.36 (range 0.31-0.37) for PBC FU. Patients with detectable tumor fraction (≥ 0.1) and TFx and OncomineTM variants had significantly lower overall survival rates (P values P = 0.002 and P < 0.0001 for the log-rank test, respectively). CONCLUSIONS The ReproSeq PGS assay is rapid, at approximately $120 per sample, providing both a sCNA profile and estimation of the tumor DNA fraction from limiting cfDNA template (300pg) and individual CTCs. The approach could be used to examine the copy number landscape over time to guide treatment decisions, support future trial designs, and be applied to low volume blood spot samples enabling remote monitoring.
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Affiliation(s)
- Rebecca C Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Karen Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Bana Ambasager
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Marc K Wadsley
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Emmanuel Acheampong
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Tumisang P Ntereke
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Qi Guo
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Gurdeep Matharu Lall
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Kelly L T Gleason
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Evie Wren
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Georgios Nteliopoulos
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Amelia J Rushton
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Jacqueline A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
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5
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Singh S, Podder PS, Russo M, Henry C, Cinti S. Tailored point-of-care biosensors for liquid biopsy in the field of oncology. LAB ON A CHIP 2022; 23:44-61. [PMID: 36321747 DOI: 10.1039/d2lc00666a] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the field of cancer detection, technologies to analyze tumors using biomarkers circulating in fluids such as blood have developed rapidly based on liquid biopsy. A proactive approach to early cancer detection can lead to more effective treatments with minimal side effects and better long-term patient survival. However, early detection of cancer is hindered by the existing limitations of conventional cancer diagnostic methods. To enable early diagnosis and regular monitoring and improve automation, the development of integrated point-of-care (POC) and biosensors is needed. This is expected to fundamentally change the diagnosis, management, and monitoring of response to treatment of cancer. POC-based techniques will provide a way to avoid complications that occur after invasive tissue biopsy, such as bleeding, infection, and pain. The aim of this study is to provide a comprehensive view of biosensors and their clinical relevance in oncology for the detection of biomarkers with liquid biopsies of proteins, miRNA, ctDNA, exosomes, and cancer cells. The preceding discussion also illustrates the changing landscape of liquid biopsy-based cancer diagnosis through nanomaterials, machine learning, artificial intelligence, wearable devices, and sensors, many of which apply POC design principles. With the advent of sensitive, selective, and timely detection of cancer, we see the field of POC technology for cancer detection and treatment undergoing a positive paradigm shift in the foreseeable future.
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Affiliation(s)
- Sima Singh
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Pritam Saha Podder
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Matt Russo
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Charles Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055 Naples, Italy
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6
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Bayle A, Peyraud F, Belcaid L, Brunet M, Aldea M, Clodion R, Dubos P, Vasseur D, Nicotra C, Geraud A, Sakkal M, Cerbone L, Blanc-Durand F, Mosele F, Romano PM, Camus MN, Soubeyran I, Khalifa E, Alame M, Blouin L, Dinart D, Bellera C, Hollebecque A, Ponce S, Loriot Y, Besse B, Lacroix L, Rouleau E, Barlesi F, Andre F, Italiano A. Liquid versus tissue biopsy for detecting actionable alterations according to ESCAT in patients with advanced cancer: A study from the French National Center for Precision Medicine (PRISM). Ann Oncol 2022; 33:1328-1331. [PMID: 36122799 DOI: 10.1016/j.annonc.2022.08.089] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/01/2022] Open
Affiliation(s)
- A Bayle
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif;; Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris;; Oncostat U1018, Inserm, Paris-Saclay University, labeled Ligue Contre le Cancer, Villejuif
| | - F Peyraud
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif;; Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux,; University of Bordeaux, Bordeaux, France
| | - L Belcaid
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif;; Department of Oncology, Rigshospitalet, The University of Copenhagen, Denmark
| | - M Brunet
- Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux
| | - M Aldea
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris;; Department of Cancer Medicine, Gustave Roussy
| | - R Clodion
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - P Dubos
- Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux
| | - D Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - C Nicotra
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - A Geraud
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M Sakkal
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - L Cerbone
- Department of Cancer Medicine, Gustave Roussy
| | | | - F Mosele
- Department of Cancer Medicine, Gustave Roussy
| | - P Martin Romano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - M Ngo Camus
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - I Soubeyran
- Department of Medical Biology and Pathology, Institut Bergonié Comprehensive Cancer Centre
| | - E Khalifa
- Department of Medical Biology and Pathology, Institut Bergonié Comprehensive Cancer Centre
| | - M Alame
- Department of Medical Biology and Pathology, Institut Bergonié Comprehensive Cancer Centre
| | - L Blouin
- Department of Medical Biology and Pathology, Institut Bergonié Comprehensive Cancer Centre
| | - D Dinart
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, Epicene team; Inserm CIC1401, Clinical and Epidemiological Research Unit,Institut Bergonié, Comprehensive Cancer Center, Bordeaux
| | - C Bellera
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, Epicene team; Inserm CIC1401, Clinical and Epidemiological Research Unit,Institut Bergonié, Comprehensive Cancer Center, Bordeaux
| | - A Hollebecque
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - S Ponce
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - Y Loriot
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif
| | - B Besse
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris;; Department of Cancer Medicine, Gustave Roussy
| | - Ludovic Lacroix
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - E Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif
| | - F Barlesi
- Department of Cancer Medicine, Gustave Roussy;; Aix Marseille University, CNRS, INSERM, CRCM, Marseille
| | - F Andre
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, Paris;; Department of Cancer Medicine, Gustave Roussy
| | - A Italiano
- Drug Development Department (DITEP) Gustave Roussy - Cancer Campus, Villejuif;; Department of Early Phase Trial Unit, Institut Bergonié Comprehensive Cancer Centre, Bordeaux,; University of Bordeaux, Bordeaux, France;.
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7
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Pascual J, Attard G, Bidard FC, Curigliano G, De Mattos-Arruda L, Diehn M, Italiano A, Lindberg J, Merker JD, Montagut C, Normanno N, Pantel K, Pentheroudakis G, Popat S, Reis-Filho JS, Tie J, Seoane J, Tarazona N, Yoshino T, Turner NC. ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2022; 33:750-768. [PMID: 35809752 DOI: 10.1016/j.annonc.2022.05.520] [Citation(s) in RCA: 219] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/16/2022] Open
Abstract
Circulating tumour DNA (ctDNA) assays conducted on plasma are rapidly developing a strong evidence base for use in patients with cancer. The European Society for Medical Oncology convened an expert working group to review the analytical and clinical validity and utility of ctDNA assays. For patients with advanced cancer, validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, and may be used in routine clinical practice, provided the limitations of the assays are taken into account. Tissue based testing remains the preferred test for many cancer patients, due to limitations of ctDNA assays detecting fusion events and copy number changes, although ctDNA assays may be routinely used when faster results will be clinically important, or when tissue biopsies are not possible or inappropriate. Reflex tumour testing should be considered following a non-informative ctDNA result, due to false negative results with ctDNA testing. In patients treated for early-stage cancers, detection of molecular residual disease (MRD) or molecular relapse (MR), has high evidence of clinical validity in anticipating future relapse in many cancers. MRD/MR detection cannot be recommended in routine clinical practice, as currently there is no evidence for clinical utility in directing treatment. Additional potential applications of ctDNA assays, under research development and not recommended for routine practice, include identifying patients not responding to therapy with early dynamic changes in ctDNA levels, monitoring therapy for the development of resistance mutations prior to clinical progression, and in screening asymptomatic people for cancer. Recommendation for reporting of results, future development of ctDNA assays, and future clinical research are made.
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Affiliation(s)
- Javier Pascual
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Gerhardt Attard
- Urological Cancer Research, University College London, London, UK
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris, France; University of Versailles Saint-Quentin-en-Yvelines (UVSQ)/Paris-Saclay University, Saint Cloud, France
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy; Division of Early Drug Development, European Institute of Oncology, IRCCS, Milano, Italy
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, US
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonie, Bordeaux, France; DITEP, Gustave Roussy, Villejuif, France; Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Jason D Merker
- Departments of Pathology and Laboratory Medicine & Genetics, UNC School of Medicine, Chapel Hill, NC, US
| | - Clara Montagut
- Medical Oncology Department, Hospital del Mar-IMIM, CIBERONC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, 'Fondazione G. Pascale' - IRCCS, Naples, Italy
| | - Klaus Pantel
- Institute for Tumour Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - George Pentheroudakis
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - Sanjay Popat
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joan Seoane
- Preclinical and Translational Research Programme, Vall d'Hebron Institute of Oncology (VHIO), ICREA, CIBERONC, Barcelona, Spain,; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Nicholas C Turner
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
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8
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Kavan S, Kruse TA, Vogsen M, Hildebrandt MG, Thomassen M. Heterogeneity and tumor evolution reflected in liquid biopsy in metastatic breast cancer patients: a review. Cancer Metastasis Rev 2022; 41:433-446. [PMID: 35286542 DOI: 10.1007/s10555-022-10023-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/07/2022] [Indexed: 02/06/2023]
Abstract
Breast cancer is a spatially and temporally dynamic disease in which differently evolving genetic clones are responsible for progression and clinical outcome. We review tumor heterogeneity and clonal evolution from studies comparing primary tumors and metastasis and discuss plasma circulating tumor DNA as a powerful real-time approach for monitoring the clonal landscape of breast cancer during treatment and recurrence. We found only a few early studies exploring clonal evolution and heterogeneity through analysis of multiregional tissue biopsies of different progression steps in comparison with circulating tumor DNA (ctDNA) from blood plasma. The model of linear progression seemed to be more often reported than the model of parallel progression. The results show complex routes to metastasis, however, and plasma most often reflected metastasis more than primary tumor. The described patterns of evolution and the polyclonal nature of breast cancer have clinical consequences and should be considered during patient diagnosis and treatment selection. Current studies focusing on the relevance of clonal evolution in the clinical setting illustrate the role of liquid biopsy as a noninvasive biomarker for monitoring clonal progression and response to treatment. In the clinical setting, circulating tumor DNA may be an ideal support for tumor biopsies to characterize the genetic landscape of the metastatic disease and to improve longitudinal monitoring of disease dynamics and treatment effectiveness through detection of residual tumor after resection, relapse, or metastasis within a particular patient.
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Affiliation(s)
- Stephanie Kavan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. .,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne Vogsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Malene G Hildebrandt
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Centre for Personalized Response Monitoring in Oncology (PREMIO), Odense University Hospital, Odense, Denmark
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9
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Chedid J, Allam S, Chamseddine N, Bou Zerdan M, El Nakib C, Assi HI. Role of circulating tumor DNA and circulating tumor cells in breast cancer: History and updates. SAGE Open Med 2022; 10:20503121221077838. [PMID: 35223029 PMCID: PMC8874178 DOI: 10.1177/20503121221077838] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Circulating tumor DNA, cell-free DNA, and circulating tumor cells have been at the epitome of recent research in breast cancer. These forms of liquid biopsies have been used in monitoring disease progression, estimating the risk of relapse, and response to treatment. Much has been done in relation to serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. Some studies have also explored their use in monitoring treatment response. As the field of liquid biopsies expands, more prospective studies are needed to tailor management in an individualistic approach. In this literature review, the authors explore the multiple uses of circulating tumor DNA and circulating tumor cells in breast cancer.
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Affiliation(s)
- Julien Chedid
- Department of Obstetrics and Gynecology, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Sabine Allam
- Faculty of Medicine, University of Balamand, Beirut, Lebanon
| | - Nathalie Chamseddine
- Department of Obstetrics and Gynecology, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Maroun Bou Zerdan
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Clara El Nakib
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hazem I Assi
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
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10
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Stadler JC, Belloum Y, Deitert B, Sementsov M, Heidrich I, Gebhardt C, Keller L, Pantel K. Current and Future Clinical Applications of ctDNA in Immuno-Oncology. Cancer Res 2022; 82:349-358. [PMID: 34815256 PMCID: PMC9397642 DOI: 10.1158/0008-5472.can-21-1718] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/06/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Testing peripheral blood for circulating tumor DNA (ctDNA) offers a minimally invasive opportunity to diagnose, characterize, and monitor the disease in individual cancer patients. ctDNA can reflect the actual tumor burden and specific genomic state of disease and thus might serve as a prognostic and predictive biomarker for immune checkpoint inhibitor (ICI) therapy. Recent studies in various cancer entities (e.g., melanoma, non-small cell lung cancer, colon cancer, and urothelial cancer) have shown that sequential ctDNA analyses allow for the identification of responders to ICI therapy, with a significant lead time to imaging. ctDNA assessment may also help distinguish pseudoprogression under ICI therapy from real progression. Developing dynamic changes in ctDNA concentrations as a potential surrogate endpoint of clinical efficacy in patients undergoing adjuvant immunotherapy is ongoing. Besides overall ctDNA burden, further ctDNA characterization can help uncover tumor-specific determinants (e.g., tumor mutational burden and microsatellite instability) of responses or resistance to immunotherapy. In future studies, standardized ctDNA assessments need to be included in interventional clinical trials across cancer entities to demonstrate the clinical utility of ctDNA as a biomarker for personalized cancer immunotherapy.
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Affiliation(s)
- Julia-Christina Stadler
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Deitert
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Sementsov
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Isabel Heidrich
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoffer Gebhardt
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Keller
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
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11
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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12
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Cucchiara F, Scarpitta R, Crucitta S, Scatena C, Arici R, Naccarato AG, Fogli S, Danesi R, Del Re M. Diagnosis and treatment monitoring in breast cancer: how liquid biopsy can support patient management. Pharmacogenomics 2022; 23:119-134. [PMID: 35006002 DOI: 10.2217/pgs-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Imaging and tissue biopsies represent the current gold standard for breast cancer diagnosis and patient management. However, these practices are time-consuming, expensive and require invasive procedures. Moreover, tissue biopsies do not capture spatial and temporal tumor heterogeneity. Conversely, liquid biopsy, which includes circulating tumor cells, circulating free nucleic acids and extracellular vesicles, is minimally invasive, easy to perform and can be repeated during a patient's follow-up. Increasing evidence also suggests that liquid biopsy can be used to efficiently screen and diagnose tumors at an early stage, and to monitor changes in the tumor molecular profile. In the present review, clinical applications and prospects are discussed.
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Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Rosa Scarpitta
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Roberta Arici
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefano Fogli
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
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13
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Sant M, Bernat-Peguera A, Felip E, Margelí M. Role of ctDNA in Breast Cancer. Cancers (Basel) 2022; 14:310. [PMID: 35053474 PMCID: PMC8773730 DOI: 10.3390/cancers14020310] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is currently classified by immunohistochemistry. However, technological advances in the detection of circulating tumor DNA (ctDNA) have made new options available for diagnosis, classification, biological knowledge, and treatment selection. Breast cancer is a heterogeneous disease and ctDNA can accurately reflect this heterogeneity, allowing us to detect, monitor, and understand the evolution of the disease. Breast cancer patients have higher levels of circulating DNA than healthy subjects, and ctDNA can be used for different objectives at different timepoints of the disease, ranging from screening and early detection to monitoring for resistance mutations in advanced disease. In early breast cancer, ctDNA clearance has been associated with higher rates of complete pathological response after neoadjuvant treatment and with fewer recurrences after radical treatments. In metastatic disease, ctDNA can help select the optimal sequencing of treatments. In the future, thanks to new bioinformatics tools, the use of ctDNA in breast cancer will become more frequent, enhancing our knowledge of the biology of tumors. Moreover, deep learning algorithms may also be able to predict breast cancer evolution or treatment sensitivity. In the coming years, continued research and the improvement of liquid biopsy techniques will be key to the implementation of ctDNA analysis in routine clinical practice.
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Affiliation(s)
- Marta Sant
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
| | - Adrià Bernat-Peguera
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eudald Felip
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Mireia Margelí
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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14
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Chen ZM, Mou Q, Wu SH, Xie Y, Salminen K, Sun JJ. Real-Time Tunable Dynamic Range for Calibration-Free Biomolecular Measurements with a Temperature-Modulated Electrochemical Aptamer-Based Sensor in an Unprocessed Actual Sample. Anal Chem 2021; 94:1397-1405. [PMID: 34962777 DOI: 10.1021/acs.analchem.1c04697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The sensing technologies for monitoring molecular analytes in biological fluids with high frequency and in real time could enable a broad range of applications in personalized healthcare and clinical diagnosis. However, due to the limited dynamic range (less than 81-fold), real-time analysis of biomolecular concentration varying over multiple orders of magnitude is a severe challenge faced by this class of analytical platforms. For the first time, we describe here that temperature-modulated electrochemical aptamer-based sensors with a dynamically adjustable calibration-free detection window could enable continuous, real-time, and accurate response for the several-hundredfold target concentration changes in unprocessed actual samples. Specifically, we could regulate the electrode surface temperature of sensors to obtain the corresponding dynamic range because of the temperature-dependent affinity variations. This temperature modulation method relies on an alternate hot and cold electrode reported by our group, whose surface could actively be heated and cooled without the need for altering ambient temperature, thus likewise applying for the flowing system. We then performed dual-frequency calibration-free measurements at different interface temperatures, thus achieving an extended detection window from 25 to 2500 μM for procaine in undiluted urine, 1-500 μM for adenosine triphosphate, and 5-2000 μM for adenosine in undiluted serum. The resulting sensor architecture could drastically expand the real-time response range accessible to these continuous, reagent-less biosensors.
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Affiliation(s)
- Zhi-Min Chen
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Qi Mou
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Sheng-Hong Wu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Yu Xie
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Kalle Salminen
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Jian-Jun Sun
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
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15
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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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16
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Childs A, Steele CD, Vesely C, Rizzo FM, Ensell L, Lowe H, Dhami P, Vaikkinen H, Luong TV, Conde L, Herrero J, Caplin M, Toumpanakis C, Thirlwell C, Hartley JA, Pillay N, Meyer T. Whole-genome sequencing of single circulating tumor cells from neuroendocrine neoplasms. Endocr Relat Cancer 2021; 28:631-644. [PMID: 34280125 PMCID: PMC8428071 DOI: 10.1530/erc-21-0179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/16/2021] [Indexed: 11/20/2022]
Abstract
Single-cell profiling of circulating tumor cells (CTCs) as part of a minimally invasive liquid biopsy presents an opportunity to characterize and monitor tumor heterogeneity and evolution in individual patients. In this study, we aimed to compare single-cell copy number variation (CNV) data with tissue and define the degree of intra- and inter-patient genomic heterogeneity. We performed next-generation sequencing (NGS) whole-genome CNV analysis of 125 single CTCs derived from seven patients with neuroendocrine neoplasms (NEN) alongside matched white blood cells (WBC), formalin-fixed paraffin-embedded (FFPE), and fresh frozen (FF) samples. CTC CNV profiling demonstrated recurrent chromosomal alterations in previously reported NEN copy number hotspots, including the prognostically relevant loss of chromosome 18. Unsupervised hierarchical clustering revealed CTCs with distinct clonal lineages as well as significant intra- and inter-patient genomic heterogeneity, including subclonal alterations not detectable by bulk analysis and previously unreported in NEN. Notably, we also demonstrated the presence of genomically distinct CTCs according to the enrichment strategy utilized (EpCAM-dependent vs size-based). This work has significant implications for the identification of therapeutic targets, tracking of evolutionary change, and the implementation of CTC-biomarkers in cancer.
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Affiliation(s)
- Alexa Childs
- UCL Cancer Institute, University College London, London, UK
| | | | - Clare Vesely
- UCL Cancer Institute, University College London, London, UK
| | | | - Leah Ensell
- UCL Cancer Institute, University College London, London, UK
| | - Helen Lowe
- UCL Cancer Institute, University College London, London, UK
| | - Pawan Dhami
- UCL Cancer Institute, University College London, London, UK
| | - Heli Vaikkinen
- UCL Cancer Institute, University College London, London, UK
| | - Tu Vinh Luong
- Department of Histopathology, Royal Free London NHS Foundation Trust, London, UK
| | - Lucia Conde
- UCL Cancer Institute, University College London, London, UK
| | - Javier Herrero
- UCL Cancer Institute, University College London, London, UK
| | - Martyn Caplin
- Department of Gastroenterology, Royal Free London NHS Foundation Trust, London, UK
| | - Christos Toumpanakis
- Department of Gastroenterology, Royal Free London NHS Foundation Trust, London, UK
| | - Christina Thirlwell
- UCL Cancer Institute, University College London, London, UK
- Department of Oncology, Royal Free London NHS Foundation Trust, London, UK
| | - John A Hartley
- UCL Cancer Institute, University College London, London, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Tim Meyer
- UCL Cancer Institute, University College London, London, UK
- Department of Oncology, Royal Free London NHS Foundation Trust, London, UK
- Correspondence should be addressed to T Meyer:
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17
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Bohers E, Viailly PJ, Jardin F. cfDNA Sequencing: Technological Approaches and Bioinformatic Issues. Pharmaceuticals (Basel) 2021; 14:ph14060596. [PMID: 34205827 PMCID: PMC8234829 DOI: 10.3390/ph14060596] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
In the era of precision medicine, it is crucial to identify molecular alterations that will guide the therapeutic management of patients. In this context, circulating tumoral DNA (ctDNA) released by the tumor in body fluids, like blood, and carrying its molecular characteristics is becoming a powerful biomarker for non-invasive detection and monitoring of cancer. Major recent technological advances, especially in terms of sequencing, have made possible its analysis, the challenge still being its reliable early detection. Different parameters, from the pre-analytical phase to the choice of sequencing technology and bioinformatic tools can influence the sensitivity of ctDNA detection.
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18
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Liu L, Yuan M, Jin Y, Zhou G, Li T, Li L, Peng H, Chen W. Tunable Dual-Effector Allostery System for Nucleic Acid Analysis with Enhanced Sensitivity and an Extended Dynamic Range. Anal Chem 2021; 93:8170-8177. [PMID: 34096261 DOI: 10.1021/acs.analchem.1c00055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the last few years, studies have demonstrated the existence of dual-effector allosteric cooperativity in nature and the mechanism underlying enhanced activation/inhibition performance. In this work, we design an artificial dual-effector allostery system for the construction of a dynamic biosensor that can achieve nucleic acid detection with superior sensitivity and across an extraordinary broad detection range. Our dual-effector allostery-regulated biosensor is based on the multibranched hybridization chain reaction (mHCR) involving three hairpins (H1, H2, and H3). In the presence of the target nucleic acid, the mHCR is initiated via cascading strand displacement events. The products of mHCR are then captured on the electrode surface based on the mechanism of the multivalent proximity ligation assay (mPLA) and the multivalent binding assay (mBA). The subsequent conjugation of streptavidin-modified horseradish peroxidase (SA-HRP) can lead to an increase in the electrochemical signal. Importantly, two distinct allosteric activation sites and two distinct allosteric inhibition sites in H1 are designed to fine-tune the nucleic acid detection sensitivity and the dynamic range. Using this new dual-effector allostery tool, we report the detection of nucleic acid at a dynamic range spanning 10-1012 aM, 11 orders of magnitude showing the broadest dynamic range reported to date with an allosteric regulation biosensor construct.
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Affiliation(s)
- Liangliang Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, P. R. China
| | - Mengmeng Yuan
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Yuxia Jin
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Guobao Zhou
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Tuqiang Li
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Lei Li
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Huaping Peng
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, P. R. China
| | - Wei Chen
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, P. R. China
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19
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Sznurkowska MK, Aceto N. The gate to metastasis: key players in cancer cell intravasation. FEBS J 2021; 289:4336-4354. [PMID: 34077633 PMCID: PMC9546053 DOI: 10.1111/febs.16046] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/19/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
Metastasis is a leading cause of cancer‐related death and consists of a sequence of events including tumor expansion, intravasation of cancer cells into the circulation, survival in the bloodstream, extravasation at distant sites, and subsequent organ colonization. Particularly, intravasation is a process whereby cancer cells transverse the endothelium and leave the primary tumor site, pioneering the metastatic cascade. The identification of those mechanisms that trigger the entry of cancer cells into the bloodstream may reveal fundamentally novel ways to block metastasis at its start. Multiple factors have been implicated in cancer progression, yet, signals that unequivocally provoke the detachment of cancer cells from the primary tumor are still under investigation. Here, we discuss the role of intrinsic properties of cancer cells, tumor microenvironment, and mechanical cues in the intravasation process, outlining studies that suggest the involvement of various factors and highlighting current understanding and open questions in the field.
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Affiliation(s)
- Magdalena K Sznurkowska
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Switzerland.,Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland
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20
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Weber ZT, Collier KA, Tallman D, Forman J, Shukla S, Asad S, Rhoades J, Freeman S, Parsons HA, Williams NO, Barroso-Sousa R, Stover EH, Mahdi H, Cibulskis C, Lennon NJ, Ha G, Adalsteinsson VA, Tolaney SM, Stover DG. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med 2021; 13:89. [PMID: 34016182 PMCID: PMC8136103 DOI: 10.1186/s13073-021-00895-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressures. In metastatic cancers, ctDNA profiling allows for simultaneous analysis of both local and distant sites of recurrence. Despite the promise of ctDNA sampling, its utility in real-time genetic monitoring remains largely unexplored. METHODS In this exploratory analysis, we characterize high-frequency ctDNA sample series collected over narrow time frames from seven patients with metastatic triple-negative breast cancer, each undergoing treatment with Cabozantinib, a multi-tyrosine kinase inhibitor (NCT01738438, https://clinicaltrials.gov/ct2/show/NCT01738438 ). Applying orthogonal whole exome sequencing, ultra-low pass whole genome sequencing, and 396-gene targeted panel sequencing, we analyzed 42 plasma-derived ctDNA libraries, representing 4-8 samples per patient with 6-42 days between samples. Integrating tumor fraction, copy number, and somatic variant information, we model tumor clonal dynamics, predict neoantigens, and evaluate consistency of genomic information from orthogonal assays. RESULTS We measured considerable variation in ctDNA tumor faction in each patient, often conflicting with RECIST imaging response metrics. In orthogonal sequencing, we found high concordance between targeted panel and whole exome sequencing in both variant detection and variant allele frequency estimation (specificity = 95.5%, VAF correlation, r = 0.949), Copy number remained generally stable, despite resolution limitations posed by low tumor fraction. Through modeling, we inferred and tracked distinct clonal populations specific to each patient and built phylogenetic trees revealing alterations in hallmark breast cancer drivers, including TP53, PIK3CA, CDK4, and PTEN. Our modeling revealed varied responses to therapy, with some individuals displaying stable clonal profiles, while others showed signs of substantial expansion or reduction in prevalence, with characteristic alterations of varied literature annotation in relation to the study drug. Finally, we predicted and tracked neoantigen-producing alterations across time, exposing translationally relevant detection patterns. CONCLUSIONS Despite technical challenges arising from low tumor content, metastatic ctDNA monitoring can aid our understanding of response and progression, while minimizing patient risk and discomfort. In this study, we demonstrate the potential for high-frequency monitoring of evolving genomic features, providing an important step toward scalable, translational genomics for clinical decision making.
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Affiliation(s)
- Zachary T Weber
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Katharine A Collier
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | - David Tallman
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Juliet Forman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sachet Shukla
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sarah Asad
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Justin Rhoades
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Samuel Freeman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Nicole O Williams
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | | | - Elizabeth H Stover
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Haider Mahdi
- Department of Obstetrics and Gynecology, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Surgery, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA
| | - Carrie Cibulskis
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Niall J Lennon
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Daniel G Stover
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA.
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA.
- Biomedical Research Tower, Room 984, Ohio State University Comprehensive Cancer Center, Stefanie Spielman Comprehensive Breast Center, Columbus, OH, 43210, USA.
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21
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Gao Y, Qiao H, Pan V, Wang Z, Li J, Wei Y, Ke Y, Qi H. Accurate genotyping of fragmented DNA using a toehold assisted padlock probe. Biosens Bioelectron 2021; 179:113079. [PMID: 33636500 DOI: 10.1016/j.bios.2021.113079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 02/03/2021] [Indexed: 11/15/2022]
Abstract
Fragmented DNA from blood plasma, i.e., cell-free DNA, has received great interest as a noninvasive diagnostic biomarker for "point-of-care" testing or liquid biopsy. Here, we present a new approach for accurate genotyping of highly fragmented DNA. Based on toehold-mediated strand displacement, a toehold-assisted padlock probe and toehold blocker were designed and demonstrated with new controllability in significantly suppressing undesired cross-reaction, promoting target recycling and point mutation detection by tuning the thermodynamic properties. Furthermore, toehold-assisted padlock probe systems were elaborately designed for 14 different single-nucleotide variants (SNVs) and were demonstrated to be able to detect low concentration of variant alleles (0.1%). In addition, a target, spanning a narrow sequence window of 29 nucleotides on average is sufficient for the toehold-assisted padlock probe system, which is valuable for the analysis of highly fragmented DNA molecules from clinical samples. We further demonstrated that the toehold-assisted padlock probe, in combination with a unique asymmetric PCR technique, could detect more target SNVs at low allele fractions (1%) in highly fragmented cfDNA. This allows accurate genotyping and provides a new commercial approach for high-resolution analysis of genetic variation.
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Affiliation(s)
- Yanmin Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, United States
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yanan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, United States
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China.
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22
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Freitas MO, Gartner J, Rangel-Pozzo A, Mai S. Genomic Instability in Circulating Tumor Cells. Cancers (Basel) 2020; 12:cancers12103001. [PMID: 33081135 PMCID: PMC7602879 DOI: 10.3390/cancers12103001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary In this review, we focus on recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability of CTCs and the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level. Abstract Circulating tumor cells (CTCs) can promote distant metastases and can be obtained through minimally invasive liquid biopsy for clinical assessment in cancer patients. Having both genomic heterogeneity and instability as common features, the genetic characterization of CTCs can serve as a powerful tool for a better understanding of the molecular changes occurring at tumor initiation and during tumor progression/metastasis. In this review, we will highlight recent advances in the detection and quantification of tumor cell heterogeneity and genomic instability in CTCs. We will focus on the contribution of chromosome instability studies to genetic heterogeneity in CTCs at the single-CTC level by discussing data from different cancer subtypes and their impact on diagnosis and precision medicine.
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Affiliation(s)
- Monique Oliveira Freitas
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Genetic Service, Institute of Paediatrics and Puericulture Martagão Gesteira (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-912, Brazil
- Clinical Medicine Postgraduate Programme, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-913, Brazil
| | - John Gartner
- Departments of Pathology and Immunology, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB R3C 2B7, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-4125 (S.M.)
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23
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Cayrefourcq L, Alix-Panabières C. Clinical relevance of liquid biopsy in breast cancer: update in 2020. Expert Rev Mol Diagn 2020; 20:913-919. [DOI: 10.1080/14737159.2020.1816828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Laure Cayrefourcq
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
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24
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Mo H, Wang X, Ma F, Qian Z, Sun X, Yi Z, Guan X, Li L, Liu B, Xu B. Genome-wide chromosomal instability by cell-free DNA sequencing predicts survival in patients with metastatic breast cancer. Breast 2020; 53:111-118. [PMID: 32738630 PMCID: PMC7503795 DOI: 10.1016/j.breast.2020.07.004] [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: 01/31/2020] [Revised: 06/22/2020] [Accepted: 07/19/2020] [Indexed: 02/05/2023] Open
Abstract
Background Genome-wide chromosomal instability, instead of specific somatic mutations or copy-number alterations in selected genes, is a significant property of cancer and may suggest a new strategy for treatment. Here we utilized cell-free DNA (cfDNA) sequencing to display the whole picture of chromosomal instability in patients with metastatic breast cancer (MBC), and evaluate its predictive value for patient survival. Methods The clinical data of 65 patients who had frozen plasma and planned to change the therapeutic regimen were retrospectively enrolled. Low-coverage whole-genome sequencing of cfDNA was performed to generate the chromosomal instability represented by chromosomal instability (CIN) score. Results Tumors with diverse status of hormone receptor and HER2 represented diverse chromosomal instability across the whole genome. According to the receiver operating characteristic curve and the statistical distribution, CIN score exceed 3881 was defined as “High”. 32 (53.3%) patients with high CIN score had similar clinicopathologic characteristics compared with low CIN score patients. The median overall survival of patients with high CIN score was 21.2 months (95% CI 14.1–28.3), which was significantly inferior to those with low CIN score (not reached, P = 0.006). Regardless of various treatment regimens, the median progression free survival in patients with high CIN score was 7.3 months, which was significantly worse than those in the low CIN score population (11.0 months, P = 0.034). Multivariate analysis revealed that CIN score was an independent prognostic factor, with hazard ratio of 3.563 (P = 0.005). Conclusions To our knowledge, this is the first study illustrating the prognostic value of chromosomal instability derived from cfDNA in MBC. Novel UCAD pipeline to profile genome-wide chromosomal instability in cfDNA. Genome-wide chromosomal instability is a robust independent prognostic biomarker. HER2 amplification was successfully identified from cfDNA in our cohort.
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Affiliation(s)
- 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
| | - Xiaobing Wang
- State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, 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.
| | - Ziliang Qian
- Prophet Genomics Inc, San Jose, USA; Suzhou Hongyuan Biotech Inc, Biobay, Suzhou, 215123, China
| | - Xiaoying Sun
- Department of Medical Oncology, Cancer Hospital of Huanxing, Beijing, China
| | - 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
| | - 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
| | - Lixi Li
- 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
| | - 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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25
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Rikkert LG, Engelaer M, Hau CM, Terstappen LWMM, Nieuwland R, Coumans FA. Rate zonal centrifugation can partially separate platelets from platelet-derived vesicles. Res Pract Thromb Haemost 2020; 4:1053-1059. [PMID: 32864556 PMCID: PMC7443435 DOI: 10.1002/rth2.12366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Centrifugation is commonly used as a first step to enrich biomarkers from blood. Biomarkers are separated on the basis of density and/or diameter. However, the centrifugation protocol affects the yield and purity of biomarkers, for example, isolation of platelets results in co-isolation with extracellular vesicles (EVs). OBJECTIVE To assess the ability of rate zonal centrifugation (RZC) to separate platelets from co-isolated EVs. METHODS Using a linear Optiprep gradient, RZC was able to separate a mixture of beads with different diameters but similar density. Next, RZC was applied to samples containing both platelets and platelet-derived EVs (n = 3). After RZC, all fractions were collected and stained with anti-CD61-Alexa 488 to measure the concentrations of platelets and platelet-derived EVs by flow cytometry. RESULTS We confirm that RZC separates polystyrene beads with diameters of 140 nm, 380 nm and 1,000 nm. Next, we show that the majority of platelets occur in fractions 8-19, whereas the majority of platelet-derived EVs are detectable in fractions 1-7. Furthermore, each fraction contains a different diameter range of platelets, which suggests that separation is indeed diameter based. CONCLUSION RZC can partially separate platelets from EVs.
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Affiliation(s)
- Linda G. Rikkert
- Department of Medical Cell BioPhysicsUniversity of TwenteEnschedeThe Netherlands
- Amsterdam UMCLaboratory of Experimental Clinical ChemistryUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam UMCUniversity of AmsterdamVesicle Observation CenterAmsterdamThe Netherlands
| | - Mendel Engelaer
- Amsterdam UMCLaboratory of Experimental Clinical ChemistryUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam UMCUniversity of AmsterdamVesicle Observation CenterAmsterdamThe Netherlands
| | - Chi M. Hau
- Amsterdam UMCLaboratory of Experimental Clinical ChemistryUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam UMCUniversity of AmsterdamVesicle Observation CenterAmsterdamThe Netherlands
| | | | - Rienk Nieuwland
- Amsterdam UMCLaboratory of Experimental Clinical ChemistryUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam UMCUniversity of AmsterdamVesicle Observation CenterAmsterdamThe Netherlands
| | - Frank A.W. Coumans
- Amsterdam UMCLaboratory of Experimental Clinical ChemistryUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam UMCUniversity of AmsterdamVesicle Observation CenterAmsterdamThe Netherlands
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26
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Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients. Cancers (Basel) 2020; 12:cancers12051084. [PMID: 32349306 PMCID: PMC7281124 DOI: 10.3390/cancers12051084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
Cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for therapy management in oncology. We aimed to establish a multimodal liquid biopsy strategy that is usable with minimized blood volume to deconvolute the genomic complexity of metastatic breast cancer. CTCs were isolated from 10ml blood of 18 hormone receptor-positive and human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer patients. cfDNA was isolated from plasma generated after CTC depletion and targeted sequencing analyses were conducted. PIK3CA and ESR1 variants were less common in CTC gDNA, while ERBB2 variants were only detected in CTC gDNA. A total of 62% of all cfDNA variants were recovered in the matched CTC gDNA, while 72% of all variants were unique in either cfDNA (14 variants) or CTC gDNA (104 variants). The percentage of patients with no detectable cfDNA variants or CTC gDNA variants was 17%/11%, but a combined analysis identified variants in 94% of all patients. In univariate and multivariate regression models, ESR1 variants in cfDNA and CTC gDNA correlated significantly with survival. We suggest a coordinated analysis of both fractions in order to provide a comprehensive genomic footprint that may contribute to identifying the most suitable therapy for each individual.
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27
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Chang S, Hur JY, Choi YL, Lee CH, Kim WS. Current status and future perspectives of liquid biopsy in non-small cell lung cancer. J Pathol Transl Med 2020; 54:204-212. [PMID: 32460474 PMCID: PMC7253954 DOI: 10.4132/jptm.2020.02.27] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
With advances in target therapy, molecular analysis of tumors is routinely required for treatment decisions in patients with advanced non-small cell lung cancer (NSCLC). Liquid biopsy refers to the sampling and analysis of circulating cell-free tumor DNA (ctDNA) in various body fluids, primarily blood. Because the technique is minimally invasive, liquid biopsies are the future in cancer management. Epidermal growth factor receptor (EGFR) ctDNA tests have been performed in routine clinical practice in advanced NSCLC patients to guide tyrosine kinase inhibitor treatment. In the near future, liquid biopsy will be a crucial prognostic, predictive, and diagnostic method in NSCLC. Here we present the current status and future perspectives of liquid biopsy in NSCLC.
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Affiliation(s)
- Sunhee Chang
- Department of Pathology, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Jae Young Hur
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
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28
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Abstract
In only few years, circulating tumor DNA (ctDNA) in breast cancer has moved from purely fundamental research to nearby daily use for treatment selection and drug-resistance assessment. Indeed, technical advances and widespread use of next-generation sequencing or digital PCR allowed for detection of very low amount of tumor DNA in bloodstream. The use of ctDNA as liquid biopsy able either to monitor tumor burden under treatment or to overcome tumor heterogeneity and identify potential targetable drivers. Time has come to define how ctDNA can be implemented for early or metastatic breast cancer management. Data from retrospective analyses of prospective trials have recently highlighted the potential advantages but also the limitations of ctDNA, in particular for patients under endocrine therapy.
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Affiliation(s)
- Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 rue d'Amiens, 76038, Rouen Cedex 1, France.
- Normandie Univ, UNIROUEN, Inserm U1245, IRON Group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France.
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29
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Kolinsky MP, Stoecklein N, Lambros M, Gil V, Rodrigues DN, Carreira S, Zafeiriou Z, de Bono JS. Genetic Analysis of Circulating Tumour Cells. Recent Results Cancer Res 2020; 215:57-76. [PMID: 31605223 DOI: 10.1007/978-3-030-26439-0_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The classification of human cancers has traditionally relied on the tissue of origin, the histologic appearance and anatomical extent of disease, otherwise referred to as grade and stage. However, this system fails to explain the highly variable clinical behaviour seen for any one cancer. Molecular characterization through techniques such as next-generation sequencing (NGS) has led to an appreciation of the extreme genetic heterogeneity that underlies most human cancers. Because of the difficulties associated with fresh tissue biopsy, interest has increased in using circulating tumour material, such as circulating tumour cells (CTCs), as a non-invasive way to access tumour tissue. CTC enumeration has been demonstrated to have prognostic value in metastatic breast, colon and prostate cancers. Recent studies have also shown that CTCs are suitable material for molecular characterization, using techniques such as reverse transcription-polymerase chain reaction (RT-PCR), fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and NGS. Furthermore, genetic analysis of CTCs may be more suitable to study tumour heterogeneity and clonal evolution than fresh tissue biopsy. Whether blood-based biopsy techniques will be accepted as a replacement to fresh tissue biopsies remains to be seen, but there is reason for optimism. While significant barriers to this acceptance exist, blood-based biopsy techniques appear to be reliable and representative alternatives to fresh tissue biopsy.
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Affiliation(s)
- Michael Paul Kolinsky
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
- Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, T61Z2, Canada
| | | | - Maryou Lambros
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Veronica Gil
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Daniel Nava Rodrigues
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Suzanne Carreira
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Zafeiris Zafeiriou
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Johann Sebastian de Bono
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK.
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30
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Abdulmawjood B, Roma-Rodrigues C, Fernandes AR, Baptista PV. Liquid biopsies in myeloid malignancies. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:1044-1061. [PMID: 35582281 PMCID: PMC9019201 DOI: 10.20517/cdr.2019.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022]
Abstract
Hematologic malignancies are the most common type of cancer affecting children and young adults, and encompass diseases, such as leukemia, lymphoma, and myeloma, all of which impact blood associated tissues such as the bone marrow, lymphatic system, and blood cells. Clinical diagnostics of these malignancies relies heavily on the use of bone marrow samples, which is painful, debilitating, and not free from risks for leukemia patients. Liquid biopsies are based on minimally invasive assessment of markers in the blood (and other fluids) and have the potential to improve the efficacy of diagnostic/therapeutic strategies in leukemia patients, providing a useful tool for the real time molecular profiling of patients. The most promising noninvasive biomarkers are circulating tumor cells, circulating tumor DNA, microRNAs, and exosomes. Herein, we discuss the role of assessing these circulating biomarkers for the understanding of tumor progression and metastasis, tumor progression dynamics through treatment and for follow-up.
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Affiliation(s)
- Bilal Abdulmawjood
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Catarina Roma-Rodrigues
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
| | - Pedro V Baptista
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, Caparica 2829-516, Portugal
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31
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Rikkert LG, van der Pol E, van Leeuwen TG, Nieuwland R, Coumans FAW. Centrifugation affects the purity of liquid biopsy-based tumor biomarkers. Cytometry A 2019; 93:1207-1212. [PMID: 30551256 PMCID: PMC6590195 DOI: 10.1002/cyto.a.23641] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 01/05/2023]
Abstract
Biomarkers in the blood of cancer patients include circulating tumor cells (CTCs), tumor-educated platelets (TEPs), tumor-derived extracellular vesicles (tdEVs), EV-associated miRNA (EV-miRNA), and circulating cell-free DNA (ccfDNA). Because the size and density of biomarkers differ, blood is centrifuged to isolate or concentrate the biomarker of interest. Here, we applied a model to estimate the effect of centrifugation on the purity of a biomarker according to published protocols. The model is based on the Stokes equation and was validated using polystyrene beads in buffer and plasma. Next, the model was applied to predict the biomarker behavior during centrifugation. The result was expressed as the recovery of CTCs, TEPs, tdEVs in three size ranges (1-8, 0.2-1, and 0.05-0.2 μm), EV-miRNA, and ccfDNA. Bead recovery was predicted with errors <18%. Most notable cofounders are the 22% contamination of 1-8 μm tdEVs for TEPs and the 8-82% contamination of <1 μm tdEVs for ccfDNA. A Stokes model can predict biomarker behavior in blood. None of the evaluated protocols produces a pure biomarker. Thus, care should be taken in the interpretation of obtained results, as, for example, results from TEPs may originate from co-isolated large tdEVs and ccfDNA may originate from DNA enclosed in <1 μm tdEVs. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Linda G Rikkert
- Medical Cell BioPhysics, University of Twente, Enschede, the Netherlands.,Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Clinical Chemistry, Amsterdam, the Netherlands.,Amsterdam UMC, University of Amsterdam, Vesicle Observation Center, Amsterdam, the Netherlands
| | - Edwin van der Pol
- Amsterdam UMC, University of Amsterdam, Vesicle Observation Center, Amsterdam, the Netherlands.,Amsterdam UMC, University of Amsterdam, Biomedical Engineering and Physics, Amsterdam, the Netherlands
| | - Ton G van Leeuwen
- Amsterdam UMC, University of Amsterdam, Vesicle Observation Center, Amsterdam, the Netherlands.,Amsterdam UMC, University of Amsterdam, Biomedical Engineering and Physics, Amsterdam, the Netherlands
| | - Rienk Nieuwland
- Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Clinical Chemistry, Amsterdam, the Netherlands.,Amsterdam UMC, University of Amsterdam, Vesicle Observation Center, Amsterdam, the Netherlands
| | - Frank A W Coumans
- Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Clinical Chemistry, Amsterdam, the Netherlands.,Amsterdam UMC, University of Amsterdam, Vesicle Observation Center, Amsterdam, the Netherlands
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32
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Lim SB, Lim CT, Lim WT. Single-Cell Analysis of Circulating Tumor Cells: Why Heterogeneity Matters. Cancers (Basel) 2019; 11:cancers11101595. [PMID: 31635038 PMCID: PMC6826423 DOI: 10.3390/cancers11101595] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/31/2022] Open
Abstract
Unlike bulk-cell analysis, single-cell approaches have the advantage of assessing cellular heterogeneity that governs key aspects of tumor biology. Yet, their applications to circulating tumor cells (CTCs) are relatively limited, due mainly to the technical challenges resulting from extreme rarity of CTCs. Nevertheless, recent advances in microfluidics and immunoaffinity enrichment technologies along with sequencing platforms have fueled studies aiming to enrich, isolate, and sequence whole genomes of CTCs with high fidelity across various malignancies. Here, we review recent single-cell CTC (scCTC) sequencing efforts, and the integrated workflows, that have successfully characterized patient-derived CTCs. We examine how these studies uncover DNA alterations occurring at multiple molecular levels ranging from point mutations to chromosomal rearrangements from a single CTC, and discuss their cellular heterogeneity and clinical consequences. Finally, we highlight emerging strategies to address key challenges currently limiting the translation of these findings to clinical practice.
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Affiliation(s)
- Su Bin Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.
| | - Chwee Teck Lim
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore.
- Office of Academic and Clinical Development, Duke-NUS Medical School, Singapore 169857, Singapore.
- IMCB NCC MPI Singapore Oncogenome Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore.
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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Abstract
As an alternative target to surgically resected tissue specimens, liquid biopsy has gained much attention over the past decade. Of the various circulating biomarkers, circulating tumor cells (CTCs) have particularly opened new windows into the metastatic cascade, with their functional, biochemical, and biophysical properties. Given the extreme rarity of intact CTCs and the associated technical challenges, however, analyses have been limited to bulk-cell strategies, missing out on clinically significant sources of information from cellular heterogeneity. With recent technological developments, it is now possible to probe genetic material of CTCs at the single-cell resolution to study spatial and temporal dynamics in circulation. Here, we discuss recent transcriptomic profiling efforts that enabled single-cell characterization of patient-derived CTCs spanning diverse cancer types. We further highlight how expression data of these putative biomarkers have advanced our understanding of metastatic spectrum and provided a basis for the development of CTC-based liquid biopsies to track, monitor, and predict the efficacy of therapy and any emergent resistance.
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Suppan C, Brcic I, Tiran V, Mueller HD, Posch F, Auer M, Ercan E, Ulz P, Cote RJ, Datar RH, Dandachi N, Heitzer E, Balic M. Untargeted Assessment of Tumor Fractions in Plasma for Monitoring and Prognostication from Metastatic Breast Cancer Patients Undergoing Systemic Treatment. Cancers (Basel) 2019; 11:E1171. [PMID: 31416207 PMCID: PMC6721524 DOI: 10.3390/cancers11081171] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to assess the prognostic and predictive value of an untargeted assessment of tumor fractions in the plasma of metastatic breast cancer patients and to compare circulating tumor DNA (ctDNA) with circulating tumor cells (CTC) and conventional tumor markers. In metastatic breast cancer patients (n = 29), tumor fractions in plasma were assessed using the untargeted mFAST-SeqS method from 127 serial blood samples. Resulting z-scores for the ctDNA were compared to tumor fractions established with the recently published ichorCNA algorithm and associated with the clinical outcome. We observed a close correlation between mFAST-SeqS z-scores and ichorCNA ctDNA quantifications. Patients with mFAST-SeqS z-scores above three (34.5%) showed significantly worse overall survival (p = 0.014) and progression-free survival (p = 0.018) compared to patients with lower values. Elevated z-score values were clearly associated with radiologically proven progression. The baseline CTC count, carcinoembryonic antigen (CEA), and cancer antigen (CA)15-5 had no prognostic impact on the outcome of patients in the analyzed cohort. This proof of principle study demonstrates the prognostic impact of ctDNA levels detected with mFAST-SeqS as a very fast and cost-effective means to assess the ctDNA fraction without prior knowledge of the genetic landscape of the tumor. Furthermore, mFAST-SeqS-based ctDNA levels provided an early means of measuring treatment response.
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Affiliation(s)
- Christoph Suppan
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Iva Brcic
- Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Verena Tiran
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Hannah D Mueller
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Florian Posch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Erkan Ercan
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria
| | - Richard J Cote
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ram H Datar
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Nadia Dandachi
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria.
- Research Unit Epigenetic and Genetic Cancer Biomarkers, Medical University of Graz, 8036 Graz, Austria.
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
- BioTechMed-Graz, 8036 Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8010 Graz, Austria.
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
- Research Unit Circulating Tumor Cells and Cancer Stem Cells, Medical University of Graz, 8036 Graz, Austria
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Wang W, Zhang W, Su L, Sang J, Wang S, Yao Y. Plasma cell-free DNA integrity: a potential biomarker to monitor the response of breast cancer to neoadjuvant chemotherapy. Transl Cancer Res 2019; 8:1531-1539. [PMID: 35116896 PMCID: PMC8799030 DOI: 10.21037/tcr.2019.08.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/09/2019] [Indexed: 12/26/2022]
Abstract
Background Although the clinical significance of neoadjuvant chemotherapy (NACT) is widely recognized, there is still no effective means to monitor the therapeutic response in real time. The present study aimed to investigate the significance of the cell-free DNA (cfDNA) concentration and integrity (cfDI) to monitor the response of breast cancer to NACT. Methods Twenty-nine patients with breast cancer receiving NACT were included in this study. Patients’ peripheral blood was drawn before, in the mid-term, and at the end of chemotherapy. The cfDNA concentration and cfDI were assessed using absolute quantitative PCR. Results The results showed that the cfDNA concentration and cfDI pre-NACT were not obviously correlated with the patients’ clinical characteristics. The mean cfDI value increased significantly when the patients received NACT (P<0.05), and an increasing cfDI was associated with tumor shrinkage and reduced Ki67 levels (P<0.05). In addition, the cfDI after NACT was inversely correlated with the number of metastatic lymph nodes, and the cfDI value of patients with a pathologically complete response was significantly higher than that of patients with distant metastasis after surgery. Conclusions This study suggested that cfDI could be used as an indicator to monitor the therapeutic response to NACT; however, more research is needed to confirm this conclusion.
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Affiliation(s)
- Wei Wang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Weijie Zhang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Lei Su
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jianfeng Sang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Yongzhong Yao
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 814] [Impact Index Per Article: 162.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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Lustberg MB, Stover DG, Chalmers JJ. Implementing Liquid Biopsies in Clinical Trials: State of Affairs, Opportunities, and Challenges. Cancer J 2019; 24:61-64. [PMID: 29601331 PMCID: PMC5880324 DOI: 10.1097/ppo.0000000000000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A primary goal of personalized medicine is to develop tumor-specific biomarkers to aid in treatment selection and to better evaluate response to targeted therapies. The assessment of circulating blood markers as surrogate real-time biopsies of disease status, termed liquid biopsies, has been under investigation. There are many different types of liquid biopsies each with different functionalities and limitations. These include tumor markers, circulating tumor cells, cell-free DNA, and extracellular vesicles including exosomes. Multiple clinical trials have evaluated liquid biopsies as prognostic biomarkers with positive results. Additional studies are underway to evaluate liquid biopsies as predictive biomarkers, pharmacodynamic biomarkers, and surrogate efficacy endpoints for treatment response evaluation. There are several challenges in and barriers to implementation of liquid biopsies into clinical trials and subsequently into routine clinical practice, which are addressed in this review.
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Affiliation(s)
- Maryam B. Lustberg
- Stefanie Spielman Comprehensive Breast Center, The Ohio State University, Columbus, OH, USA
| | - Daniel G Stover
- Stefanie Spielman Comprehensive Breast Center, The Ohio State University, Columbus, OH, USA
| | - Jeff J Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, 151 W. Woodruff Ave., Columbus, OH, 43210, USA
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39
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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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Zhang Y, Mi X, Tan X, Xiang R. Recent Progress on Liquid Biopsy Analysis using Surface-Enhanced Raman Spectroscopy. Theranostics 2019; 9:491-525. [PMID: 30809289 PMCID: PMC6376192 DOI: 10.7150/thno.29875] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Traditional tissue biopsy is limited in understanding heterogeneity and dynamic evolution of tumors. Instead, analyzing circulating cancer markers in various body fluids, commonly referred to as "liquid biopsy", has recently attracted remarkable interest for their great potential to be applied in non-invasive early cancer screening, tumor progression monitoring and therapy response assessment. Among the various approaches developed for liquid biopsy analysis, surface-enhanced Raman spectroscopy (SERS) has emerged as one of the most powerful techniques based on its high sensitivity, specificity, tremendous spectral multiplexing capacity for simultaneous target detection, as well as its unique capability for obtaining intrinsic fingerprint spectra of biomolecules. In this review, we will first briefly explain the mechanism of SERS, and then introduce recently reported SERS-based techniques for detection of circulating cancer markers including circulating tumor cells, exosomes, circulating tumor DNAs, microRNAs and cancer-related proteins. Cancer diagnosis based on SERS analysis of bulk body fluids will also be included. In the end, we will summarize the "state of the art" technologies of SERS-based platforms and discuss the challenges of translating them into clinical settings.
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Affiliation(s)
- Yuying Zhang
- School of Medicine, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials for Ministry of Education, Nankai University, 300071 Tianjin, China
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Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Diefenbach RJ, Lee JH, Kefford RF, Rizos H. Evaluation of commercial kits for purification of circulating free DNA. Cancer Genet 2018; 228-229:21-27. [DOI: 10.1016/j.cancergen.2018.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/27/2018] [Accepted: 08/19/2018] [Indexed: 12/11/2022]
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Nelep C, Eberhardt J. Automated rare single cell picking with the ALS cellcelector™. Cytometry A 2018; 93:1267-1270. [PMID: 30184320 PMCID: PMC6586056 DOI: 10.1002/cyto.a.23568] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/19/2018] [Accepted: 06/28/2018] [Indexed: 01/02/2023]
Abstract
Molecular analysis of rare single cells like circulating tumor cells (CTCs) from whole blood patient samples bears multiple challenges. One of those challenges is the efficient and ideally loss-free isolation of CTCs over contaminating white and red blood cells. While there is a multitude of commercial and non-commercial systems available for the enrichment of CTCs their cell output does not deliver the purity most molecular analysis methods require. Here we describe the ALS CellCelector™ which can solve this challenge allowing the retrieval of 100% pure single CTCs from blood processed by different upstream enrichment techniques. It is a multifunctional, extremely flexible system for automated screening of cell culture plates, Petri dishes, and microscope slides. Fixed or live single cells or multicellular clusters detected during screening can be picked out of those plates automatically. The complete scan and picking process is fully documented hence allowing highest standardization and reproducibility of all processes. Use of CellCelector allowed the isolation of pure single tumor cells or clusters from liquid biopsies of breast, prostate, ovarian, colorectal, lung, and brain cancers for their subsequent molecular analysis. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Mathé E, Hays JL, Stover DG, Chen JL. The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources. Yearb Med Inform 2018; 27:211-222. [PMID: 30157526 PMCID: PMC6115204 DOI: 10.1055/s-0038-1667085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The aim is to provide a comprehensive review of state-of-the art omics approaches, including proteomics, metabolomics, cell-free DNA, and patient cohort matching algorithms in precision oncology. METHODS In the past several years, the cancer informatics revolution has been the beneficiary of a data explosion. Different complementary omics technologies have begun coming into their own to provide a more nuanced view of the patient-tumor interaction beyond that of DNA alterations. A combined approach is beneficial to the patient as nearly all new cancer therapeutics are designed with an omics biomarker in mind. Proteomics and metabolomics provide us with a means of assaying in real-time the response of the tumor to treatment. Circulating cell-free DNA may allow us to better understand tumor heterogeneity and interactions with the host genome. RESULTS Integration of increasingly available omics data increases our ability to segment patients into smaller and smaller cohorts, thereby prompting a shift in our thinking about how to use these omics data. With large repositories of patient omics-outcomes data being generated, patient cohort matching algorithms have become a dominant player. CONCLUSIONS The continued promise of precision oncology is to select patients who are most likely to benefit from treatment and to avoid toxicity for those who will not. The increased public availability of omics and outcomes data in patients, along with improved computational methods and resources, are making precision oncology a reality.
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Affiliation(s)
- Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - John L. Hays
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, USA
| | - Daniel G. Stover
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James L. Chen
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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Khatami F, Tavangar SM. Circulating tumor DNA (ctDNA) in the era of personalized cancer therapy. J Diabetes Metab Disord 2018; 17:19-30. [PMID: 30288382 PMCID: PMC6154523 DOI: 10.1007/s40200-018-0334-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023]
Abstract
The heterogeneity of tumor is considered as a major difficulty to victorious personalized cancer medicine. There is an extremeneed of consistent response evaluation for in vivo tumor heterogeneity anditscoupledconflict mechanisms. In this occasion researchers will be able to keep pace withpredictive, preventive, personalized, and Participatory (P4) medicine for cancer managements. In fact tumor heterogeneity is a central part of cancer evolution,soin order to progress in understanding of the dynamics within a tumor some diagnostic apparatus should be improved. Latest molecular techniques like Next generation Sequencing (NGS) and ultra-deep sequencing could disclose some clones within a liquid tumor biopsy which mainly responsible of treatment resistance. Circulating tumor DNA (ctDNA) as a main component of liquid biopsy is agifted biomarker for cancer mutation tracking as well as profiling. Personalized medicine facilitate learning regarding to genetic pools of tumor and their possible respond to treatment which could be much easier by using of ctDNA.With this information, cliniciansarelooking forward to find the best strategies for prevention, screening, and treatment in the way of precision medicine. Currently, numerous clinical efficacy of such informative improved treatment are in hand. Here we represent the review of plasma-derived ctDNA studies use in personalized cancer managements.
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Affiliation(s)
- Fatemeh Khatami
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Tavangar
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Departments of Pathology, Doctor Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Beasley A, Isaacs T, Khattak MA, Freeman JB, Allcock R, Chen FK, Pereira MR, Yau K, Bentel J, Vermeulen T, Calapre L, Millward M, Ziman MR, Gray ES. Clinical Application of Circulating Tumor Cells and Circulating Tumor DNA in Uveal Melanoma. JCO Precis Oncol 2018; 2:1700279. [PMID: 32913999 PMCID: PMC7446501 DOI: 10.1200/po.17.00279] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To evaluate the feasibility of using circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) for the management of uveal melanoma (UM). Patients and Methods Low-coverage whole-genome sequencing was used to determine somatic chromosomal copy number alterations (SCNAs) in primary UM tumors, ctDNA, and whole-genome amplified CTCs. CTCs were immunocaptured using an antimelanoma-associated chondroitin sulfate antibody conjugated to magnetic beads and immunostained for melanoma antigen recognised by T cells 1 (MART1)/glycoprotein 100 (gp100)/S100 calcium-binding protein β (S100β). ctDNA was quantified using droplet digital polymerase chain reaction assay for mutations in the GNAQ, GNA11, PLCβ4, and CYSLTR2 genes. Results SCNA analysis of CTCs and ctDNA isolated from a patient with metastatic UM showed good concordance with the enucleated primary tumor. In a cohort of 30 patients with primary UM, CTCs were detected in 58% of patients (one to 37 CTCs per 8 mL of blood), whereas only 26% of patients had detectable ctDNA (1.6 to 29 copies/mL). The presence of CTCs or ctDNA was not associated with tumor size or other prognostic markers. However, the frequent detection of CTCs in patients with early-stage UM supports a model in which CTCs can be used to derive tumor-specific SCNA relevant for prognosis. Monitoring of ctDNA after treatment of the primary tumor allowed detection of metastatic disease earlier than 18F-labeled fluorodeoxyglucose positron emission tomography in two patients. Conclusion The presence of CTCs in localized UM can be used to ascertain prognostic SCNA, whereas ctDNA can be used to monitor patients for early signs of metastatic disease. This study paves the way for the analysis of CTCs and ctDNA as a liquid biopsy that will assist with treatment decisions in patients with UM.
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Affiliation(s)
- Aaron Beasley
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Timothy Isaacs
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Muhammad A Khattak
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - James B Freeman
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Richard Allcock
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Fred K Chen
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Michelle R Pereira
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Kyle Yau
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Jaqueline Bentel
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Tersia Vermeulen
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Leslie Calapre
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Michael Millward
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Melanie R Ziman
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Elin S Gray
- , , , , , , and , Edith Cowan University, Joondalup; , , , , , , , and , University of Western Australia, Crawley; and , Sir Charles Gairdner Hospital; , Lions Eye Institute, Nedlands; and , Royal Perth Hospital, Perth; , Perth Retina, West Leederville; and , , and Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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47
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Wang W, Kong P, Ma G, Li L, Zhu J, Xia T, Xie H, Zhou W, Wang S. Characterization of the release and biological significance of cell-free DNA from breast cancer cell lines. Oncotarget 2018; 8:43180-43191. [PMID: 28574818 PMCID: PMC5522137 DOI: 10.18632/oncotarget.17858] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
In breast cancer, cell-free DNA (cfDNA) has been proven to be a diagnostic and prognostic biomarker. However, there have been few studies on the origin and biological significance of cfDNA. In this study, we assessed the release pattern of cfDNA from breast cancer cell lines under different culture conditions and investigated the biological significance of cfDNA. The cfDNA concentration increased rapidly (6 h) after passage, decreased gradually, and was then maintained at a relatively stable level after 24 h. In addition, the cfDNA concentration did not correlate with the amount of apoptotic and necrotic cells. Interestingly, if more cells were in the G1 phase, more cfDNA was detected (p < 0.01) and the cfDNA concentration correlated positively with the percent of cells in the G1 phase (p < 0.05). We observed that cells could release cfDNA actively, but not exclusively, via exosomes. Furthermore, we showed that cfDNA could stimulate hormone receptor-positive breast cancer cell proliferation by activating the TLR9-NF-κB-cyclin D1 pathway. In conclusion, cfDNA is released from breast cancer mainly by active secretion, and cfDNA could stimulate proliferation of breast cancer cells.
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Affiliation(s)
- Wei Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Peng Kong
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Ge Ma
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Li Li
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Jin Zhu
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Tiansong Xia
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Wenbin Zhou
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
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48
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Manier S, Park J, Capelletti M, Bustoros M, Freeman SS, Ha G, Rhoades J, Liu CJ, Huynh D, Reed SC, Gydush G, Salem KZ, Rotem D, Freymond C, Yosef A, Perilla-Glen A, Garderet L, Van Allen EM, Kumar S, Love JC, Getz G, Adalsteinsson VA, Ghobrial IM. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun 2018; 9:1691. [PMID: 29703982 PMCID: PMC5923255 DOI: 10.1038/s41467-018-04001-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/29/2022] Open
Abstract
Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.
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Affiliation(s)
- S Manier
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Hematology Department, CHU, Univ. Lille, 59000, Lille, France.,INSERM UMR-S1172, 59000, Lille, France
| | - J Park
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - M Capelletti
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - M Bustoros
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S S Freeman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Ha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - J Rhoades
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C J Liu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Huynh
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - S C Reed
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Gydush
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - K Z Salem
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - D Rotem
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - C Freymond
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Yosef
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - A Perilla-Glen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - L Garderet
- Department of Hematology, St-Antoine University Hospital, Paris, 75000, France
| | - E M Van Allen
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - S Kumar
- Department of Hematology, Mayo Clinic, Rochester, MN, 55902, USA
| | - J C Love
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - G Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - V A Adalsteinsson
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - I M Ghobrial
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Brigham and Women's Hospital, Boston, MA, 02115, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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49
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Gorgannezhad L, Umer M, Islam MN, Nguyen NT, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. LAB ON A CHIP 2018; 18:1174-1196. [PMID: 29569666 DOI: 10.1039/c8lc00100f] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.
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Affiliation(s)
- Lena Gorgannezhad
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
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50
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Ma F, Zhu W, Guan Y, Yang L, Xia X, Chen S, Li Q, Guan X, Yi Z, Qian H, Yi X, Xu B. ctDNA dynamics: a novel indicator to track resistance in metastatic breast cancer treated with anti-HER2 therapy. Oncotarget 2018; 7:66020-66031. [PMID: 27602761 PMCID: PMC5323211 DOI: 10.18632/oncotarget.11791] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Most studies utilizing circulating tumor DNA (ctDNA) to monitor disease interrogated only one or a few genes and failed to develop workable criteria to inform clinical practice. We evaluated the feasibility of detecting resistance to anti-HER2 therapy by serial gene-panel ctDNA sequencing. RESULTS Primary therapeutic resistance was identified in 6 out of 14 patients with events of progressive disease. For this subset comparison of pre- and post-treatment ctDNA assay results revealed that HER2 amplification concurred with disease progression (4/6, 66.7%). Mutations in TP53 (3/6, 50.0%) and genes implicated in the PI3K/mTOR pathway (3/6, 50.0%) were also dominant markers of resistance. Together, resistance to HER2 blockade should be indicated during treatment if any of the following situations applies: 1) recurrence or persistence of HER2 amplification in the blood; 2) emergence or ≥20% increase in the fraction of mutations in any of these resistance-related genes including TP53/PIK3CA/MTOR/PTEN. Compared with CT scans, dynamic ctDNA profiling utilizing pre-defined criteria was sensitive in identifying drug resistance (sensitivity 85.7%, specificity 55.0%), with a concordance rate up to 82.1%. Besides, the ctDNA criteria had a discriminating role in the prognosis of HER2-positive metastatic breast cancer. METHODS 52 plasma samples were prospectively collected from 18 patients with HER2-positive metastatic breast cancer who were treated with an oral anti-HER1/HER2 tyrosine kinase inhibitor (ClinicalTrials.gov NCT01937689). ctDNA was assayed by gene-panel target-capture next-generation sequencing. CONCLUSIONS Longitudinal gene-panel ctDNA sequencing could be exploited to determine resistance and guide the precise administration of anti-HER2 targeted therapy in the metastatic setting.
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Affiliation(s)
- Fei Ma
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Zhu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | - Xuefeng Xia
- Houston Methodist Research Institute, Weill Cornell School of Medicine, Houston, TX, USA
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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