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Mishra M, Ahmed R, Das DK, Pramanik DD, Dash SK, Pramanik A. Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers. ACS Biomater Sci Eng 2024. [PMID: 38950521 DOI: 10.1021/acsbiomaterials.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.
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Affiliation(s)
- Mahima Mishra
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
| | - Rubai Ahmed
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Deepak Kumar Das
- Department of Chemistry and Nanoscience, GLA University, Mathura, 281406 Uttar Pradesh, India
| | | | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Arindam Pramanik
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
- School of Medicine, University of Leeds, Leeds LS53RL, United Kingdom
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Bardol T, Dujon AM, Taly V, Dunyach-Remy C, Lavigne JP, Costa-Silva B, Kurma K, Eslami-S Z, Cayrefourcq L, Canivet C, Muscari F, Bournet B, Alix-Panabières C. Early detection of pancreatic cancer by liquid biopsy "PANLIPSY": a french nation-wide study project. BMC Cancer 2024; 24:709. [PMID: 38853244 PMCID: PMC11163786 DOI: 10.1186/s12885-024-12463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Pancreatic cancer, predominantly characterized by ductal adenocarcinoma (PDAC) accounts for 90% of cases and is the fourth leading cause of cancer-related deaths globally. Its incidence is notably increasing. This poor prognosis is primarily due to late-stage diagnosis (approximately 70% to 80% of patients are diagnosed at an advanced stage), aggressive tumor biology, and low sensitivity to chemotherapy. Consequently, it is crucial to identify and develop a simple, feasible and reproducible blood-based signature (i.e., combination of biomarkers) for early detection of PDAC. METHODS The PANLIPSY study is a multi-center, non-interventional prospective clinical trial designed to achieve early detection of PDAC with high specificity and sensitivity, using a combinatorial approach in blood samples. These samples are collected from patients with resectable, borderline or locally advanced, and metastatic stage PDAC within the framework of the French Biological and Clinical Database for PDAC cohort (BACAP 2). All partners of the BACAP consortium are eligible to participate. The study will include 215 PDAC patients, plus 25 patients with benign pancreatic conditions from the PAncreatic Disease Cohort of TOuLouse (PACTOL) cohort, and 115 healthy controls, totaling 355 individuals. Circulating biomarkers will be collected in a total volume of 50 mL of blood, divided into one CellSave tube (10 mL), two CELL-FREE DNA BCT® preservative tubes (18 mL), and five EDTA tubes (22 mL in total). Samples preparation will adhere to the guidelines of the European Liquid Biopsy Society (ELBS). A unique feature of the study is the AI-based comparison of these complementary liquid biopsy biomarkers. Main end-points: i) to define a liquid biopsy signature that includes the most relevant circulating biomarkers, ii) to validate the multi-marker panel in an independent cohort of healthy controls and patients, with resectable PDAC, and iii) to establish a unique liquid biopsy biobank for PDAC study. DISCUSSION The PANLIPSY study is a unique prospective non-interventional clinical trial that brings together liquid biopsy experts. The aim is to develop a biological signature for the early detection of PDAC based on AI-assisted detection of circulating biomarkers in blood samples (CTCs, ctDNA, EVs, circulating immune system, circulating cell-free nucleosomes, proteins, and microbiota). TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT06128343 / NCT05824403. Registration dates: June 8,2023 and April 21, 2023.
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Affiliation(s)
- Thomas Bardol
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France.
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
| | - Antoine M Dujon
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia
| | - Valerie Taly
- Équipe Labélisée Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Université Paris Cité, UMR-S1138, CNRS SNC5096, Paris, France
- METHYS Dx, 67 Rue Saint-Jacques, Paris, France
| | - Catherine Dunyach-Remy
- Department of Microbiology and Hospital Hygiene Bacterial Virulence and Chronic Infections, University of Montpellier CHU Nîmes, INSERM U1047, Nîmes, France
| | - Jean-Philippe Lavigne
- Department of Microbiology and Hospital Hygiene Bacterial Virulence and Chronic Infections, University of Montpellier CHU Nîmes, INSERM U1047, Nîmes, France
| | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038, Lisbon, Portugal
| | - Keerthi Kurma
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Zahra Eslami-S
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Laure Cayrefourcq
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Cindy Canivet
- Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 Avenue Jean Poulhès, Cedex 9 50032, 31059, Toulouse, TSA, France
| | - Fabrice Muscari
- Digestive Surgery and Liver Transplantation Department, Toulouse University Hospital, Toulouse, France
| | - Barbara Bournet
- Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 Avenue Jean Poulhès, Cedex 9 50032, 31059, Toulouse, TSA, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France.
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
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Duffy MJ, Crown J. Circulating tumor DNA (ctDNA): can it be used as a pan-cancer early detection test? Crit Rev Clin Lab Sci 2024; 61:241-253. [PMID: 37936529 DOI: 10.1080/10408363.2023.2275150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023]
Abstract
Circulating tumor DNA (ctDNA, DNA shed by cancer cells) is emerging as one of the most transformative cancer biomarkers discovered to-date. Although potentially useful at all the phases of cancer detection and patient management, one of its most exciting possibilities is as a relatively noninvasive pan-cancer screening test. Preliminary findings with ctDNA tests such as Galleri or CancerSEEK suggest that they have high specificity (> 99.0%) for malignancy. Their sensitivity varies depending on the type of cancer and stage of disease but it is generally low in patients with stage I disease. A major advantage of ctDNA over existing screening strategies is the potential ability to detect multiple cancer types in a single test. A limitation of most studies published to-date is that they are predominantly case-control investigations that were carried out in patients with a previous diagnosis of malignancy and that used apparently healthy subjects as controls. Consequently, the reported sensitivities, specificities and positive predictive values might be lower if the tests are used for screening in asymptomatic populations, that is, in the population where these tests are likely be employed. To demonstrate clinical utility in an asymptomatic population, these tests must be shown to reduce cancer mortality without causing excessive overdiagnosis in a large randomized prospective randomized trial. Such trials are currently ongoing for Galleri and CancerSEEK.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
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Liu J, Bian T, She B, Liu L, Sun H, Zhang Q, Zhu J, Zhang J, Liu Y. Evaluating the comprehensive diagnosis efficiency of lung cancer, including measurement of SHOX2 and RASSF1A gene methylation. BMC Cancer 2024; 24:282. [PMID: 38429660 PMCID: PMC10908052 DOI: 10.1186/s12885-024-12022-1] [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: 07/05/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Methylation of the promoters of SHOX2 and RASSF1A (LungMe®) exhibits promise as a potential molecular biomarker for diagnosing lung cancer. This study sought to assess the aberrant methylation of SHOX2 and RASSF1A in broncho-exfoliated cells (BEC) and compare it with conventional cytology, histology examination, immunohistochemistry, and serum tumor markers to evaluate the overall diagnostic efficiency for lung cancer. This study recruited 240 patients, including 185 malignant cases and 55 benign cases. In our observation, we noted a slight reduction in the detection sensitivity, however, the ΔCt method exhibited a significant enhancement in specificity when compared to Ct judgment. Consequently, the ΔCt method proves to be a more appropriate approach for interpreting methylation results. The diagnostic sensitivity of cytology and histology was in ranged from 20.0%-35.1% and 42.9%-80%, respectively, while the positive detection rate of LungMe® methylation ranged from 70.0% to 100%. Additionally, our findings indicate a higher prevalence of SHOX2( +) among patients exhibiting medium and high expression of Ki67 (P < 0.01), as opposed to those with low expression of Ki67, but RASSF1A methylation did not show this phenomenon (P = 0.35). Furthermore, CEA, SCCA, and CYFRA21-1 showed positive detection rates of 48.8%, 26.2%, and 55.8%, respectively. Finally, we present a comprehensive lung cancer diagnostic work-up, including LumgMe® methylation. The combined analysis of SHOX2 and RASSF1A methylation serves as a powerful complement and extension to conventional methods, enhancing the accuracy of a lung cancer diagnosis with satisfactory sensitivity and specificity.
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Affiliation(s)
- Jian Liu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China
- Medical School of Nantong University, Nantong, 226001, China
| | - Bin She
- Academic Development, Shanghai Methyldia Technology Co. Ltd, Tellgen Corporation, No. 412 Huiqing Road, Shanghai, 201203, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China
| | - Qing Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China
| | - Jun Zhu
- Department of Cardio-Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Jianguo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China.
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, China.
- Medical School of Nantong University, Nantong, 226001, China.
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Leong SY, Lok WW, Goh KY, Ong HB, Tay HM, Su C, Kong F, Upadya M, Wang W, Radnaa E, Menon R, Dao M, Dalan R, Suresh S, Lim DWT, Hou HW. High-Throughput Microfluidic Extraction of Platelet-free Plasma for MicroRNA and Extracellular Vesicle Analysis. ACS NANO 2024; 18:6623-6637. [PMID: 38348825 DOI: 10.1021/acsnano.3c12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Cell-free RNAs and extracellular vesicles (EVs) are valuable biomarkers in liquid biopsies, but they are prone to preanalytical variabilities such as nonstandardized centrifugation or ex vivo blood degradation. Herein, we report a high-throughput and label-free inertial microfluidic device (ExoArc) for isolation of platelet-free plasma from blood for RNA and EV analysis. Unlike conventional inertial microfluidic devices widely used for cell sorting, a submicrometer size cutoff (500 nm) was achieved which completely removed all leukocytes, RBCs, platelets, and cellular debris based on differential lateral migration induced by Dean vortices. The single-step operation also reduced platelet-associated miRNAs (∼2-fold) compared to centrifugation. We clinically validated ExoArc for plasma miRNA profiling (39 samples) and identified a 7-miRNA panel that detects non-small cell lung cancer with ∼90% sensitivity. ExoArc was also coupled with size exclusion chromatography (SEC) to isolate EVs within 50 min with ∼10-fold higher yield than ultracentrifugation. As a proof-of-concept for EV-based transcriptomics analysis, we performed miRNA analysis in healthy and type 2 diabetes mellitus (T2DM) subjects (n = 3 per group) by coupling ExoArc and ExoArc+SEC with quantitative polymerase chain reaction (RT-qPCR) assay. Among 293 miRNAs detected, plasmas and EVs showed distinct differentially expressed miRNAs in T2DM subjects. We further demonstrated automated in-line EV sorting from low volume culture media for continuous EV monitoring. Overall, the developed ExoArc offers a convenient centrifugation-free workflow to automate plasma and EV isolation for point-of-care diagnostics and quality control in EV manufacturing.
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Affiliation(s)
- Sheng Yuan Leong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Wan Wei Lok
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Kah Yee Goh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583
| | - Hong Boon Ong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Hui Min Tay
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Chengxun Su
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Fang Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Megha Upadya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Wei Wang
- Singapore Institute of Manufacturing Technology (SIMTech), Agency for Science, Technology and Research (A*STAR), Singapore 138634
| | - Enkhtuya Radnaa
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1062, United States
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1062, United States
| | - Ming Dao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rinkoo Dalan
- Endocrine and Diabetes, Tan Tock Seng Hospital, Singapore 308433
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232
| | - Subra Suresh
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- School of Material Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Darren Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673
- Duke-NUS Medical School, Singapore 169857
| | - Han Wei Hou
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232
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Giunta EF, Malapelle U, Russo A, De Giorgi U. Blood-based liquid biopsy in advanced prostate cancer. Crit Rev Oncol Hematol 2024; 194:104241. [PMID: 38122919 DOI: 10.1016/j.critrevonc.2023.104241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Prostate cancer is characterized by several genetic alterations which could impact prognosis and therapeutic decisions in the advanced disease. Tissue biopsy is still considered the gold standard approach for molecular characterization in prostate cancer, but it has several limitations, including the possibility of insufficient/inadequate tumor tissue to be analyzed. Blood-based liquid biopsy is a non-invasive method to investigate tumor cell derivatives in the bloodstream, being a valid alternative to tissue biopsy for molecular characterization but also for predictive and/or prognostic purposes. In this review, we analyze the most relevant evidence in this field, focusing on clinically relevant targets such as HRD genetic alterations and also focusing on the differences between tissue and liquid biopsy in light of the data from the latest clinical trials.
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Affiliation(s)
- Emilio Francesco Giunta
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy.
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Ugo De Giorgi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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Ntzifa A, Lianidou E. Pre-analytical conditions and implementation of quality control steps in liquid biopsy analysis. Crit Rev Clin Lab Sci 2023; 60:573-594. [PMID: 37518938 DOI: 10.1080/10408363.2023.2230290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Over the last decade, great advancements have been made in the field of liquid biopsy through extensive research and the development of new technologies that facilitate the use of liquid biopsy for cancer patients. This is shown by the numerous liquid biopsy tests that gained clearance by the US Food and Drug Administration (FDA) in recent years. Liquid biopsy has significantly altered cancer treatment by providing clinicians with powerful and immediate information about therapeutic decisions. However, the clinical integration of liquid biopsy is still challenging and there are many critical factors to consider prior to its implementation into routine clinical practice. Lack of standardization due to technical challenges and the definition of the clinical utility of specific assays further complicates the establishment of Standard Operating Procedures (SOPs) in liquid biopsy. Harmonization of laboratories to established guidelines is of major importance to overcome inter-lab variabilities observed. Quality control assessment in diagnostic laboratories that offer liquid biopsy testing will ensure that clinicians can base their therapeutic decisions on robust results. The regular participation of laboratories in external quality assessment schemes for liquid biopsy testing aims to promptly pinpoint deficiencies and efficiently educate laboratories to improve their quality of services. Accreditation of liquid biopsy diagnostic laboratories based on the ISO15189 standard in Europe or by CLIA/CAP accreditation procedures in the US is the best way to achieve the adaptation of liquid biopsy into the clinical setting by assuring reliable results for the clinicians and their cancer patients. Nowadays, various organizations from academia, industry, and regulatory agencies collaborate to set a framework that will include all procedures from the pre-analytical phase and the analytical process to the final interpretation of results. In this review, we underline several challenges in the analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) concerning standardization of protocols, quality control assessment, harmonization of laboratories, and compliance to specific guidelines that need to be thoroughly considered before liquid biopsy enters the clinic.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Serrano MJ, Rolfo C, Expósito-Hernandez J, Garrido-Navas C, Lopez-Hidalgo J, Denninghoff V. Circulating tumor cells in cancer-risk populations as a cancer interception tool. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 381:113-129. [PMID: 37739481 DOI: 10.1016/bs.ircmb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Cancer interception (CI) is a new approach to cancer prevention and treatment in a cancer-risk population that aims to detect and treat pre-tumoral stages. It has several potential advantages over traditional cancer diagnosis and monitoring methods because it is non-invasive, making it less painful and risky than conventional biopsy procedures. The circulating tumor cells (CTCs), liquid biopsy family members, are essential for the CI approach; then, the liquid biopsy (LB) is used as a CI tool. LB can be performed frequently because of its easy sampling and early pathological stages, which allow repeated non-invasive monitoring of cancer progression and response to treatment. CTCs have been found in the bloodstream of several types of cancer patients, including in early-stage cancer and premalignant lesions, suggesting a tumor development role in cancer's early stages. This chapter will present foundational scientific studies addressing CI and the clinical impact of CTC screening in a population at risk for cancer.
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Affiliation(s)
- María José Serrano
- GENYO Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain; IBS Granada, Biosanitary Research Institute, Spain; Comprehensive Oncology Division, Virgen de las Nieves University Hospital, Granada, Spain.
| | - Christian Rolfo
- Center for Thoracic Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, United States
| | - José Expósito-Hernandez
- GENYO Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain; IBS Granada, Biosanitary Research Institute, Spain; Comprehensive Oncology Division, Virgen de las Nieves University Hospital, Granada, Spain
| | - Carmen Garrido-Navas
- IBS Granada, Biosanitary Research Institute, Spain; Comprehensive Oncology Division, Virgen de las Nieves University Hospital, Granada, Spain
| | - Javier Lopez-Hidalgo
- Department of Pathological Anatomy, Faculty of Medicine, University of Granada, Spain
| | - Valeria Denninghoff
- GENYO Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain; Molecular-Clinical Lab - University of Buenos Aires (UBA) - National Council for Scientific and Technical Research (CONICET), Argentina.
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11
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Sala A, Cameron JM, Brennan PM, Crosbie EJ, Curran T, Gray E, Martin-Hirsch P, Palmer DS, Rehman IU, Rattray NJW, Baker MJ. Global serum profiling: an opportunity for earlier cancer detection. J Exp Clin Cancer Res 2023; 42:207. [PMID: 37580713 PMCID: PMC10426107 DOI: 10.1186/s13046-023-02786-y] [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: 06/03/2023] [Accepted: 07/30/2023] [Indexed: 08/16/2023] Open
Abstract
The advances in cancer research achieved in the last 50 years have been remarkable and have provided a deeper knowledge of this disease in many of its conceptual and biochemical aspects. From viewing a tumor as a 'simple' aggregate of mutant cells and focusing on detecting key cell changes leading to the tumorigenesis, the understanding of cancer has broadened to consider it as a complex organ interacting with its close and far surroundings through tumor and non-tumor cells, metabolic mechanisms, and immune processes. Metabolism and the immune system have been linked to tumorigenesis and malignancy progression along with cancer-specific genetic mutations. However, most technologies developed to overcome the barriers to earlier detection are focused solely on genetic information. The concept of cancer as a complex organ has led to research on other analytical techniques, with the quest of finding a more sensitive and cost-effective comprehensive approach. Furthermore, artificial intelligence has gained broader consensus in the oncology community as a powerful tool with the potential to revolutionize cancer diagnosis for physicians. We herein explore the relevance of the concept of cancer as a complex organ interacting with the bodily surroundings, and focus on promising emerging technologies seeking to diagnose cancer earlier, such as liquid biopsies. We highlight the importance of a comprehensive approach to encompass all the tumor and non-tumor derived information salient to earlier cancer detection.
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Affiliation(s)
| | | | - Paul M Brennan
- Translational Neurosurgery, Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Division of Gynecology, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Tom Curran
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Ewan Gray
- Independent Health Economics Consultant, Edinburgh, UK
| | - Pierre Martin-Hirsch
- Gynecological Oncology, Clinical Research Facility, Lancashire Teaching Hospitals, Preston, PR2 9HT, UK
| | - David S Palmer
- Dxcover Limited, Glasgow, G1 1XW, UK
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Ihtesham U Rehman
- School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Nicholas J W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, G4 0RE, UK
| | - Matthew J Baker
- Dxcover Limited, Glasgow, G1 1XW, UK.
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK.
- School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK.
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12
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Sato Y, Futamura M, Tanaka Y, Tsuchiya H, Fukada M, Higashi T, Yasufuku I, Asai R, Tajima JY, Kiyama S, Hatakeyama H, Morishita M, Hirotsu T, Luccio ED, Ishihara T, Matsuhashi N, Yoshida K. Clinical Possibility of Caenorhabditis elegans as a Novel Evaluation Tool for Esophageal Cancer Patients Receiving Chemotherapy: A Prospective Study. Cancers (Basel) 2023; 15:3870. [PMID: 37568686 PMCID: PMC10417676 DOI: 10.3390/cancers15153870] [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: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis elegans (C. elegans) possesses a sophisticated sense of smell and is used for a novel cancer screening test that utilizes the chemotaxis index. We designed a single-institution, prospective study to confirm the ability of Nematode Nose (N-NOSE) to determine preoperative chemotherapy's efficacy for esophageal cancer patients. PATIENTS AND METHODS We investigated the predictability of N-NOSE screening for the clinical effects of preoperative chemotherapy for esophageal cancer patients receiving radical surgery. The index reduction score (IRS) was calculated via the chemotaxis of C. elegans at three points: before treatment, before surgery, and after surgery, and its clinical relevance was examined. RESULT Thirty-nine patients with esophageal cancer were enrolled from August 2020 to December 2021, and 30 patients receiving radical surgery were examined. Complete response or partial response was achieved in 23 cases (76.7%). When the target of the treatment effect was complete response only, the prediction accuracies of the IRS calculated by area under the curve was 0.85 (95% Confidence interval: 0.62-1) in clinically achieving complete response group, and the sensitivity and specificity were 1 and 0.63, respectively. CONCLUSION Index reduction score using N-NOSE screening may reflect the efficacy of chemotherapy for esophageal cancer patients. A large-scale prospective study at multiple centers is desired in the future.
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Affiliation(s)
- Yuta Sato
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Manabu Futamura
- Department of Breast Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Yoshihiro Tanaka
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Hiroshi Tsuchiya
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Masahiro Fukada
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Toshiya Higashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Itaru Yasufuku
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Ryuichi Asai
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Jesse Yu Tajima
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Shigeru Kiyama
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Hideyuki Hatakeyama
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Masayo Morishita
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Takaaki Hirotsu
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Eric di Luccio
- Hirotsu Bio Science Inc., 22F The New Otani Garden Court, 4-1 Kioicho Chiyoda-ku, Tokyo 102-0094, Japan
| | - Takuma Ishihara
- Innovative and Clinical Research Promotion Center, Gifu University Hospital, Gifu 501-1194, Japan
| | - Nobuhisa Matsuhashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Kazuhiro Yoshida
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
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13
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Bronkhorst AJ, Holdenrieder S. Cell-Free Nucleic Acids: Physico-Chemical Properties, Analytical Considerations, and Clinical Applications. Diagnostics (Basel) 2023; 13:2312. [PMID: 37443705 DOI: 10.3390/diagnostics13132312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Human body fluids are rich sources of cell-free nuclear material, which exhibits unique characteristics [...].
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Affiliation(s)
- Abel J Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany
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14
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Dhani H, Hinestrosa JP, Izaguirre-Carbonell J, Balcer HI, Kurzrock R, Billings PR. Case Report: Early detection of pancreatic pre-cancer lesion in multimodal approach with exosome liquid biopsy. Front Oncol 2023; 13:1170513. [PMID: 37251939 PMCID: PMC10210587 DOI: 10.3389/fonc.2023.1170513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Background The detection of pancreatic ductal adenocarcinoma (PDAC) lesions at pre-cancerous or early-stages is critical to improving patient survival. We have developed a liquid biopsy test (ExoVita®) based on the measurement of protein biomarkers in cancer-derived exosomes. The high sensitivity and specificity of the test for early-stage PDAC has the potential to improve a patient's diagnostic journey in hopes to impact patient outcomes. Methods Exosome isolation was performed using alternating current electric (ACE) field applied to the patient plasma sample. Following a wash to eliminate unbound particles, the exosomes were eluted from the cartridge. A downstream multiplex immunoassay was performed to measure proteins of interest on the exosomes, and a proprietary algorithm provided a score for probability of PDAC. Results We describe the case of a 60-year-old healthy non-Hispanic white male with acute pancreatitis who underwent numerous invasive diagnostic procedures that failed to detect radiographic evidence of pancreatic lesions. Following the results of our exosome-based liquid biopsy test showing "High Likelihood of PDAC", in addition to KRAS and TP53 mutations, the patient decided to undergo a robotic pancreaticoduodenectomy (Whipple) procedure. Surgical pathology confirmed the diagnosis of high-grade intraductal papillary mucinous neoplasm (IPMN), which was consistent with the results of our ExoVita® test. The patient's post-operative course was unremarkable. At five-month follow-up, the patient continued to recover well without complications, in addition to a repeat ExoVita test which demonstrated "Low Likelihood of PDAC". Conclusion This case report highlights how a novel liquid biopsy diagnostic test based on the detection of exosome protein biomarkers allowed early diagnosis of a high-grade precancerous lesion for PDAC and improved patient outcome.
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Affiliation(s)
- Harmeet Dhani
- Biological Dynamics, Inc., San Diego, CA, United States
- Georgetown University, Washington, DC, United States
| | | | | | | | - Razelle Kurzrock
- Medical College of Wisconsin, Milwaukee, WI, United States
- Worldwide Innovative Network (WIN) Consortium for Precision Medicine, Villejuif, France
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15
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Armakolas A, Kotsari M, Koskinas J. Liquid Biopsies, Novel Approaches and Future Directions. Cancers (Basel) 2023; 15:1579. [PMID: 36900369 PMCID: PMC10000663 DOI: 10.3390/cancers15051579] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.
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Affiliation(s)
- Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Maria Kotsari
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - John Koskinas
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
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16
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Horgan D, Hamdi Y, Lal JA, Nyawira T, Meyer S, Kondji D, Francisco NM, De Guzman R, Paul A, Bernard B, Reddy Nallamalla K, Park WY, Triapthi V, Tripathi R, Johns A, Singh MP, Phipps ME, Dube F, Rasheed HMA, Kozaric M, Pinto JA, Doral Stefani S, Aponte Rueda ME, Fujita Alarcon R, Barrera-Saldana HA. Framework for Adoption of Next-Generation Sequencing (NGS) Globally in the Oncology Area. Healthcare (Basel) 2023; 11:healthcare11030431. [PMID: 36767006 PMCID: PMC9914369 DOI: 10.3390/healthcare11030431] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Radical new possibilities of improved treatment of cancer are on offer from an advanced medical technology already demonstrating its significance: next-generation sequencing (NGS). This refined testing provides unprecedentedly precise diagnoses and permits the use of focused and highly personalized treatments. However, across regions globally, many cancer patients will continue to be denied the benefits of NGS as long as some of the yawning gaps in its implementation remain unattended. The challenges at the regional and national levels are linked because putting the solutions into effect is highly dependent on cooperation between regional- and national-level cooperation, which could be hindered by shortfalls in interpretation or understanding. The aim of the paper was to define and explore the necessary conditions for NGS and make recommendations for effective implementation based on extensive exchanges with policy makers and stakeholders. As a result, the European Alliance for Personalised Medicine (EAPM) developed a maturity framework structured around demand-side and supply-side issues to enable interested stakeholders in different countries to self-evaluate according to a common matrix. A questionnaire was designed to identify the current status of NGS implementation, and it was submitted to different experts in different institutions globally. This revealed significant variability in the different aspects of NGS uptake. Within different regions globally, to ensure those conditions are right, this can be improved by linking efforts made at the national level, where patients have needs and where care is delivered, and at the global level, where major policy initiatives in the health field are underway or in preparation, many of which offer direct or indirect pathways for building those conditions. In addition, in a period when consensus is still incomplete and catching up is needed at a political level to ensure rational allocation of resources-even within individual countries-to enable the best ways to make the necessary provisions for NGS, a key recommendation is to examine where closer links between national and regional actions could complement, support, and mutually reinforce efforts to improve the situation for patients.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
- Correspondence:
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
- Department of Genetics and Cell Biology, GROW School of Oncology and Developmental Biology, Faculty of Health, Medicine and Life Sciences, Institute for Public Health Genomics, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Teresia Nyawira
- National Commission for Science, Technology and Innovation in Kenya (NACOSTI), Nairobi 00100, Kenya
| | | | - Dominique Kondji
- Health & Development Communication, Building Capacity for Better Health in Africa, Yaounde P.O. Box 2032, Cameroon
| | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda 3635, Angola
| | - Roselle De Guzman
- Oncology and Pain Management Section, Manila Central University—Filemon D. Tanchoco Medical Foundation Hospital, Caloocan 1400, Philippines
| | - Anupriya Paul
- Department of Mathematics and Statistics, Faculty of Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Branka Bernard
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia
| | | | - Woong-Yang Park
- Samsung Medical Center, Samsung Genome Institute, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Vijay Triapthi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Ravikant Tripathi
- Department Health Government of India, Ministry of Labor, New Delhi 110001, India
| | - Amber Johns
- Cancer Division, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Sydney 2010, Australia
| | - Mohan P. Singh
- Center of Biotechnology, University of Allahabad, Allahabad 211002, India
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - France Dube
- Precision Medicine and Breast Cancer Department, Astra Zeneca, 1800 Concord Pike, Wilmington, DE 19803, USA
| | | | - Marta Kozaric
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
| | - Joseph A. Pinto
- Center for Basic and Translational Research, Auna Ideas, Lima 15036, Peru
| | | | | | - Ricardo Fujita Alarcon
- Centro de Genética y Biología Molecular, Universidad de San Martín de Porres, Lima 15024, Peru
| | - Hugo A. Barrera-Saldana
- Innbiogem SC/Vitagenesis SA at National Laboratory for Services of Research, Development, and Innovation for the Pharma and Biotech Industries (LANSEIDI) of CONACyT Vitaxentrum Group, Monterrey 64630, Mexico
- Schools of Medicine and Biology, Autonomous University of Nuevo Leon, Monterrey 66451, Mexico
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Temraz S, Nasr R, Mukherji D, Kreidieh F, Shamseddine A. Liquid Biopsy Derived Circulating Tumor Cells and Circulating Tumor DNA as Novel Biomarkers in Hepatocellular Carcinoma. Expert Rev Mol Diagn 2022; 22:507-518. [PMID: 35758097 DOI: 10.1080/14737159.2022.2094706] [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: 12/13/2022]
Abstract
INTRODUCTION The diagnosis of hepatocellular carcinoma (HCC) is made at a relatively advanced stage resulting in poor prognosis. Alpha-fetoprotein and liver ultrasound have limited accuracy as biomarkers in HCC. Liver biopsy provides information on tumor biology; however, it is invasive and holds high threat of tumor seeding. Thus, more accurate and less invasive approaches are needed. AREAS COVERED Highly sensitive liquid biopsy assays have made possible the detection and analysis of cells or organelles such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and tumor-derived exosomes. Here, we focus on CTCs and ctDNA components of liquid biopsy and their clinical application as diagnostic, prognostic and predictive biomarkers in HCC. Unlike tissue biopsy, liquid biopsy involves attaining a sample at several time frames in an easy and a non-invasive manner. They have been efficacious in detecting and classifying cancer, in predicting treatment response, in monitoring disease relapse and in identifying mechanisms of resistance to targeted therapies. EXPERT OPINION Although interesting and highly promising, liquid biopsy techniques still have many obstacles to overcome before their wide spread clinical application sees the light. It is expected that these techniques will be incorporated into traditional methodologies for better diagnostic, predictive and prognostic results.
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Affiliation(s)
- Sally Temraz
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiology, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Deborah Mukherji
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Firas Kreidieh
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Ali Shamseddine
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
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The Early Detection of Breast Cancer Using Liquid Biopsies: Model Estimates of the Benefits, Harms, and Costs. Cancers (Basel) 2022; 14:cancers14122951. [PMID: 35740615 PMCID: PMC9220983 DOI: 10.3390/cancers14122951] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 01/20/2023] Open
Abstract
Simple Summary Breast cancer screening is associated with benefits, such as mortality reduction and improved quality of life, and harms, such as false-positive results, overdiagnoses, and costs. Novel screen tests could be considered to reduce the harms and increase the benefits of screening. Liquid biopsies have been proposed as a novel method for the early detection of breast cancer. However, studies show that liquid biopsies based on cell-free DNA have a low sensitivity for early-stage breast cancer. Using the microsimulation model MISCAN-Fadia, we model the benefits, harms, and costs of the early detection of breast cancer using liquid biopsies for varying levels of liquid biopsy sensitivity and specificity. We found that liquid biopsies are unlikely to be an alternative to digital mammography, given the test performance based on a CCGA substudy. When liquid biopsies are unable to detect the precursor lesion of breast cancer—ductal carcinoma in situ (DCIS)—they need to be able to detect small, early-stage tumors, with high specificity, at low costs in order to be an alternative to digital mammography. We estimated a maximum liquid biopsy price of USD 187, which is substantially lower than currently listed prices. Abstract Breast cancer screening is associated with harms, such as false-positives and overdiagnoses, and, thus, novel screen tests can be considered. Liquid biopsies have been proposed as a novel method for the early detection of cancer, but low cell-free DNA tumor fraction might pose a problem for the use in population screening. Using breast cancer microsimulation model MISCAN-Fadia, we estimated the outcomes of using liquid biopsies in breast cancer screening in women aged 50 to 74 in the United States. For varying combinations of test sensitivity and specificity, we quantify the impact of the use of liquid biopsies on the harms and benefits of screening, and we estimate the maximum liquid biopsy price for cost-effective implementation in breast cancer screening at a cost-effectiveness threshold of USD 50,000. We investigate under what conditions liquid biopsies could be a suitable alternative to digital mammography and compare these conditions to a CCGA substudy. Outcomes were compared to digital mammography screening, and include mortality reduction, overdiagnoses, quality-adjusted life-years (QALYs), and the maximum price of a liquid biopsy for cost-effective implementation. When liquid biopsies are unable to detect DCIS, a large proportion of overdiagnosed cases is prevented but overall breast cancer mortality reduction and quality of life are lower, and costs are higher compared to digital mammography screening. Liquid biopsies prices should be restricted to USD 187 per liquid biopsy depending on test performance. Overall, liquid biopsies that are unable to detect ductal carcinoma in situ (DCIS) need to be able to detect small, early-stage tumors, with high specificity, at low costs in order to be an alternative to digital mammography. Liquid biopsies might be more suitable as an addition to digital mammography than as an alternative.
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Multi Cancer Early Detection by Using Circulating Tumor DNA—The Galleri Test. Reply to Klein et al. The Promise of Multicancer Early Detection. Comment on “Pons-Belda et al. Can Circulating Tumor DNA Support a Successful Screening Test for Early Cancer Detection? The Grail Paradigm. Diagnostics 2021, 11, 2171”. Diagnostics (Basel) 2022; 12:diagnostics12051244. [PMID: 35626399 PMCID: PMC9141547 DOI: 10.3390/diagnostics12051244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
We recently published some concerns with new technologies which are based on circulating tumor DNA (ctDNA) for early cancer detection. Most of our published criticism, including a commentary in this journal, has focused on tests developed by the biotechnology company GRAIL (their commercial product is also known as The Galleri Test). Scientists from GRAIL provided explanations and rebuttals to our criticism. They also posed some questions. Here, we reiterate our position and provide rebuttals, explanations and answers to these questions. We believe that constructive scientific debates, like this one, can profoundly contribute to advancements in scientific fields such as early cancer detection.
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Klein EA, Beer TM, Seiden M. The Promise of Multicancer Early Detection. Comment on Pons-Belda et al. Can Circulating Tumor DNA Support a Successful Screening Test for Early Cancer Detection? The Grail Paradigm. Diagnostics 2021, 11, 2171. Diagnostics (Basel) 2022; 12:diagnostics12051243. [PMID: 35626398 PMCID: PMC9141107 DOI: 10.3390/diagnostics12051243] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 12/20/2022] Open
Abstract
Multicancer Early Detection (MCED) represents a new and exciting paradigm for the early detection of cancer, which is the leading cause of death worldwide. Current screening tests, recommended for only five cancer types (breast, lung, colon, cervical, and prostate), are limited by a lack of complete adherence to guideline-based use and by the fact that they have cumulative high false positive rates. MCED tests agnostically detect cancer signals in the blood with good sensitivity and low false positive rates, can predict the cancer site of origin with high accuracy, can detect highly lethal cancers that have no current screening tests, and promise to improve cancer screening by improving efficiency and reducing the overall number needed to screen. Herein we outline this promise and clarify several published misconceptions about this field.
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Affiliation(s)
- Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, 9500 Euclid Ave, Q10-1, Cleveland, OH 44195, USA
- Correspondence:
| | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health & Science University, CH-14R, 3303 SW Bond Ave, Portland, OR 97239, USA;
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The potential of liquid biopsy in the management of cancer patients. Semin Cancer Biol 2022; 84:69-79. [DOI: 10.1016/j.semcancer.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
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