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Zhang Y, Du H, Wang N, Wang L, Huang Y. An update of clinical value of circulating tumor DNA in esophageal cancer: a systematic review and meta-analysis. BMC Cancer 2024; 24:129. [PMID: 38267901 PMCID: PMC10809487 DOI: 10.1186/s12885-024-11879-6] [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: 08/22/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a deadly disease with limited therapeutic options. Although circulating tumor DNA (ctDNA) could be a promising tool in this regard, the availiable evidence is limited. We performed a systematic review and meta-analysis to summarize the clinical applicability of the next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) technology on the ctDNA detection of the EC and listed the current challenges. METHODS We systematically searched MEDLINE (via PubMed), Embase (via OVID), ISI Web of Science database and Cochrane Library from January, 2000 to April, 2023. Progression-free survival (PFS) and overall survival (OS) were set as primary outcome endpoints. Pathologic response was evaluated by tumor regression grade (TRG), according to the eighth edition of the American Joint Committee on Cancer (AJCC). Major pathologic regression (MPR) was defined as TRG 1 and 2. The MPR was set as secondary endpoint. Hazard rate (HR) and associated 95% CI were used as the effect indicators the association between ctDNA and prognosis of EC. MPR rates were also calculated. Fixed-effect model (Inverse Variance) or random-effect model (Mantel-Haenszel method) was performed depending on the statistically heterogeneity. RESULTS Twenty-two studies, containing 1144 patients with EC, were included in this meta-analysis. The results showed that OS (HR = 3.87; 95% CI, 2.86-5.23) and PFS (HR = 4.28; 95% CI, 3.34-5.48) were shorter in ctDNA-positive patients. In the neoadjuvant therapy, the sensitivity analysis showed the clarified HR of ctDNA-positive was 1.13(95% CI, 1.01-1.28). We also found that TP53, NOTCH1, CCND1 and CNKN2A are the most frequent mutation genes. CONCLUSIONS Positive ctDNA is associated with poor prognosis, which demonstrated clinical value of ctDNA. Longitudinal ctDNA monitoring showed potential prognostic value in the neoadjuvant therapy. In an era of precision medicine, ctDNA could be a promising tool to individualize treatment planning and to improve outcomes in EC. PROSPERO REGISTRATION NUMBER CRD42023412465.
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Affiliation(s)
- Yaozhong Zhang
- Department of Infectious diseases, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huazhen Du
- Department of Emergency, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Na Wang
- Department of Molecular Biology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Wang
- Department of Thoracic Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajie Huang
- Department of Medical oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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2
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Verner EL, Jackson JB, Severson E, Valkenburg KC, Greer AE, Riley DR, Sausen M, Maddox C, McGregor PM, Karandikar A, Hastings SB, Previs RA, Reddy VP, Jensen TJ, Ramkissoon SH. Validation of the Labcorp Plasma Focus Test to Facilitate Precision Oncology Through Cell-Free DNA Genomic Profiling of Solid Tumors. J Mol Diagn 2023; 25:477-489. [PMID: 37068734 DOI: 10.1016/j.jmoldx.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Genomic profiling is critical for precision oncology to guide treatment decisions. Liquid biopsy testing is a complementary approach to tissue testing, particularly when tissue is not readily available. The Labcorp Plasma Focus test is a circulating cell-free DNA genomic profiling test that identifies actionable variants in solid cancers, including non-small-cell lung, colorectal, melanoma, breast, esophageal, gastroesophageal junction, and gastric cancers. This study highlights the analytical validation of the test, including accuracy compared with orthogonal methods, as well as sensitivity, specificity, precision, reproducibility, and repeatability. Concordance with orthogonal methods showed percent positive agreement of 98.7%, 89.3%, and 96.2% for single nucleotide variants (SNVs), insertion/deletions (indels), and copy number amplifications (CNAs), respectively, and 100.0% for translocations and microsatellite instability (MSI). Analytical sensitivity revealed a median limit of detection of 0.7% and 0.6% for SNVs and indels, 1.4-fold for CNAs, 0.5% variant allele frequency for translocations, and 0.6% for MSI. Specificity was >99% for SNVs/indels and 100% for CNAs, translocations, and MSI. Average positive agreement from precision, reproducibility, and repeatability experiments was 97.5% and 88.9% for SNVs/indels and CNAs, and 100% for translocations and MSI. Taken together, these data show that the Labcorp Plasma Focus test is a highly accurate, sensitive, and specific approach for cell-free DNA genomic profiling to supplement tissue testing and inform treatment decisions.
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Affiliation(s)
- Ellen L Verner
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland.
| | | | - Eric Severson
- Enterprise Oncology, Labcorp, Durham, North Carolina
| | | | - Amy E Greer
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
| | - David R Riley
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
| | - Mark Sausen
- Personal Genome Diagnostics (PGDx), Baltimore, Maryland
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3
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Grizzi G, Salati M, Bonomi M, Ratti M, Holladay L, De Grandis MC, Spada D, Baiocchi GL, Ghidini M. Circulating Tumor DNA in Gastric Adenocarcinoma: Future Clinical Applications and Perspectives. Int J Mol Sci 2023; 24:ijms24119421. [PMID: 37298371 DOI: 10.3390/ijms24119421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Gastric cancer (GC) is still one of the most aggressive cancers with a few targetable alterations and a dismal prognosis. A liquid biopsy allows for identifying and analyzing the DNA released from tumor cells into the bloodstream. Compared to tissue-based biopsy, liquid biopsy is less invasive, requires fewer samples, and can be repeated over time in order to longitudinally monitor tumor burden and molecular changes. Circulating tumor DNA (ctDNA) has been recognized to have a prognostic role in all the disease stages of GC. The aim of this article is to review the current and future applications of ctDNA in gastric adenocarcinoma, in particular, with respect to early diagnosis, the detection of minimal residual disease (MRD) following curative surgery, and in the advanced disease setting for treatment decision choice and therapeutic monitoring. Although liquid biopsies have shown potentiality, pre-analytical and analytical steps must be standardized and validated to ensure the reproducibility and standardization of the procedures and data analysis methods. Further research is needed to allow the use of liquid biopsy in everyday clinical practice.
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Affiliation(s)
| | - Massimiliano Salati
- Department of Oncology and Hematology, University Hospital of Modena, 41124 Modena, Italy
| | - Maria Bonomi
- Oncology Unit, ASST Cremona, 26100 Cremona, Italy
| | | | - Lauren Holladay
- Anne Burnett Marion School of Medicine, Texas Christian University, Fort Worth, TX 76129, USA
| | | | | | | | - Michele Ghidini
- Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
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4
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Labiano I, Huerta AE, Arrazubi V, Hernandez-Garcia I, Mata E, Gomez D, Arasanz H, Vera R, Alsina M. State of the Art: ctDNA in Upper Gastrointestinal Malignancies. Cancers (Basel) 2023; 15:1379. [PMID: 36900172 PMCID: PMC10000247 DOI: 10.3390/cancers15051379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising non-invasive source to characterize genetic alterations related to the tumor. Upper gastrointestinal cancers, including gastroesophageal adenocarcinoma (GEC), biliary tract cancer (BTC) and pancreatic ductal adenocarcinoma (PADC) are poor prognostic malignancies, usually diagnosed at advanced stages when no longer amenable to surgical resection and show a poor prognosis even for resected patients. In this sense, ctDNA has emerged as a promising non-invasive tool with different applications, from early diagnosis to molecular characterization and follow-up of tumor genomic evolution. In this manuscript, novel advances in the field of ctDNA analysis in upper gastrointestinal tumors are presented and discussed. Overall, ctDNA analyses can help in early diagnosis, outperforming current diagnostic approaches. Detection of ctDNA prior to surgery or active treatment is also a prognostic marker that associates with worse survival, while ctDNA detection after surgery is indicative of minimal residual disease, anticipating in some cases the imaging-based detection of progression. In the advanced setting, ctDNA analyses characterize the genetic landscape of the tumor and identify patients for targeted-therapy approaches, and studies show variable concordance levels with tissue-based genetic testing. In this line, several studies also show that ctDNA serves to follow responses to active therapy, especially in targeted approaches, where it can detect multiple resistance mechanisms. Unfortunately, current studies are still limited and observational. Future prospective multi-center and interventional studies, carefully designed to assess the value of ctDNA to help clinical decision-making, will shed light on the real applicability of ctDNA in upper gastrointestinal tumor management. This manuscript presents a review of the evidence available in this field up to date.
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Affiliation(s)
- Ibone Labiano
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Ana Elsa Huerta
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Virginia Arrazubi
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Irene Hernandez-Garcia
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Elena Mata
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - David Gomez
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Hugo Arasanz
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Ruth Vera
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
| | - Maria Alsina
- Oncobiona Group, Navarrabiomed-Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
- Medical Oncology Department, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008 Pamplona, Spain
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5
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Mencel J, Slater S, Cartwright E, Starling N. The Role of ctDNA in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14205105. [PMID: 36291888 PMCID: PMC9600786 DOI: 10.3390/cancers14205105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary DNA release from tumour cells (call circulating tumour DNA) into the blood stream can be found in patients with gastric cancer through a blood test call a liquid biopsy. This less invasive test can assess the genetic make-up of tumours to provide important information on the mechanisms of cancer development, identify mutations which can be targeted with drugs and could be used to screen for patients with gastric cancer. This article will review the current and future uses of liquid biopsies in gastric cancer. Abstract Circulating tumour DNA (ctDNA) has potential applications in gastric cancer (GC) with respect to screening, the detection of minimal residual disease (MRD) following curative surgery, and in the advanced disease setting for treatment decision making and therapeutic monitoring. It can provide a less invasive and convenient method to capture the tumoural genomic landscape compared to tissue-based next-generation DNA sequencing (NGS). In addition, ctDNA can potentially overcome the challenges of tumour heterogeneity seen with tissue-based NGS. Although the evidence for ctDNA in GC is evolving, its potential utility is far reaching and may shape the management of this disease in the future. This article will review the current and future applications of ctDNA in GC.
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6
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Paschold L, Binder M. Circulating Tumor DNA in Gastric and Gastroesophageal Junction Cancer. Curr Oncol 2022; 29:1430-1441. [PMID: 35323320 PMCID: PMC8947276 DOI: 10.3390/curroncol29030120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Tumor cells shed DNA into the plasma. “Liquid biopsy” analysis of mutations or other genomic alterations in circulating cell-free DNA (cfDNA) may provide us with a tool to detect minimal residual cancer, comprehensively profile the genomic tumor landscape in search of druggable targets, and monitor cancers non-invasively over time for treatment failure or emerging treatment-resistant tumor subclones. While liquid biopsies have not yet entered routine clinical management in patients with gastric and gastroesophageal junction cancers, this group of diseases may benefit from such advanced diagnostic tools due to their pronounced genetic spatiotemporal heterogeneity and limitations in imaging sensitivity. Moreover, as the armamentarium of targeted treatment approaches and immunotherapies expands, cfDNA analyses may reveal their utility not only as a biomarker of response but also for precision monitoring. In this review, we discuss the different applications of cfDNA analyses in patients with gastric and gastroesophageal junction cancer and the technical challenges that such liquid biopsies have yet to overcome.
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Affiliation(s)
| | - Mascha Binder
- Correspondence: ; Tel.: +49-345-557-4972; Fax: +49-345-557-2950
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7
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Killcoyne S, Fitzgerald RC. Evolution and progression of Barrett's oesophagus to oesophageal cancer. Nat Rev Cancer 2021; 21:731-741. [PMID: 34545238 DOI: 10.1038/s41568-021-00400-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
Cancer cells are shaped through an evolutionary process of DNA mutation, cell selection and population expansion. Early steps in this process are driven by a set of mutated driver genes and structural alterations to the genome through copy number gains or losses. Oesophageal adenocarcinoma (EAC) and the pre-invasive tissue, Barrett's oesophagus (BE), provide an ideal example in which to observe and study this evolution. BE displays early genomic instability, specifically in copy number changes that may later be observed in EAC. Furthermore, these early changes result in patterns of progression (that is, 'born bad', gradual or catastrophic) that may help to describe the evolution of EAC. As only a small proportion of patients with BE will go on to develop cancer, a better understanding of these patterns and the resulting genomic changes should improve early detection in EAC and may provide clues for the evolution of cancer more broadly.
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Affiliation(s)
- Sarah Killcoyne
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK.
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8
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Chidambaram S, Markar SR. Clinical utility and applicability of circulating tumor DNA testing in esophageal cancer: a systematic review and meta-analysis. Dis Esophagus 2021; 35:6324875. [PMID: 34286823 PMCID: PMC8832526 DOI: 10.1093/dote/doab046] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022]
Abstract
Esophageal cancer is an aggressive malignancy with a relatively poor prognosis even after multimodality therapy. Currently, patients undergo a series of investigations that can be invasive and costly or pose secondary risks to their health. In other malignancies, liquid biopsies of circulating tumor DNA (ctDNA) are used in clinical practice for diagnostic and surveillance purposes. This systematic review summarizes the latest evidence for the clinical applicability of ctDNA technology in esophageal cancer. A systematic review of the literature was performed using MEDLINE, EMBASE, the Cochrane Review and Scopus databases. Articles were evaluated for the use of ctDNA for diagnosis and monitoring of patients with esophageal cancer. Quality assessment of studies was performed using the QUADAS-2 tool. A meta-analysis was performed to assess the diagnostic accuracy of sequencing methodologies. We included 15 studies that described the use of ctDNA technology in the qualitative synthesis and eight studies involving 414 patients in the quantitative analysis. Of these, four studies assessed its utility in cancer diagnosis, while four studies evaluated its use for prognosis and monitoring. The pooled sensitivity and specificity for diagnostic studies were 71.0% (55.7-82.6%) and 98.6% (33.9-99.9%), while the pooled sensitivity and specificity for surveillance purposes were 48.9% (29.4-68.8%) and 95.5% (90.6-97.9%). ctDNA technology is an acceptable method for diagnosis and monitoring with a moderate sensitivity and high specificity that is enhanced in combination with current imaging methods. Further work should demonstrate the practical integration of ctDNA in the diagnostic and surveillance clinical pathway.
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Affiliation(s)
- Swathikan Chidambaram
- Address correspondence to: Sheraz R. Markar, Division of Surgery, Department of Surgery & Cancer, Imperial College London, Academic Surgical Unit, 10th Floor QEQM, St Mary’s Hospital, South Wharf Road, London W2 1NY, UK.
| | - Sheraz R Markar
- Department of Surgery and Cancer, Imperial College London, London, UK,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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9
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Fong CYK, Chau I. Harnessing biomarkers of response to improve therapy selection in esophago-gastric adenocarcinoma. Pharmacogenomics 2021; 22:703-726. [PMID: 34120461 PMCID: PMC8265282 DOI: 10.2217/pgs-2020-0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
Advanced esophago-gastric (OG) adenocarcinomas have a high mortality rate and new therapeutic options are urgently required. Despite recent advances in understanding the molecular characteristics of OG cancers, tumor heterogeneity poses a challenge in developing new therapeutics capable of improving patient outcomes. Consequently, chemotherapy remains the mainstay of systemic treatment, with the HER2 being the only predictive biomarker routinely targeted in clinical practice. Recent data indicate that immunotherapy will be incorporated into first-line chemotherapy, but further research is required to refine patient selection. This review will summarize the clinical strategies being evaluated to utilize our knowledge of predictive biomarkers with reference to novel therapeutics, and discuss the barriers to implementing precision oncology in OG adenocarcinoma.
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Affiliation(s)
- Caroline YK Fong
- The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Ian Chau
- The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT, UK
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Paracchini L, D’Incalci M, Marchini S. Liquid Biopsy in the Clinical Management of High-Grade Serous Epithelial Ovarian Cancer-Current Use and Future Opportunities. Cancers (Basel) 2021; 13:2386. [PMID: 34069200 PMCID: PMC8156052 DOI: 10.3390/cancers13102386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
The lack of a sensitive and specific biomarker and the limits relating to the single primary tumor sampling make it difficult to monitor high-grade serous epithelial ovarian cancer (HGS-EOC) over time and to capture those alterations that are potentially useful in guiding clinical decisions. To overcome these issues, liquid biopsy has emerged as a very promising tool for HGS-EOC. The analysis of circulating tumor DNA appears to be feasible and studies assessing specific pathogenic mutations (i.e., TP53) or copy number alterations have shown a sufficient degree of sensitivity and specificity to be realistically used to monitor the effectiveness of antitumor therapy. Liquid biopsy can also provide potential important information on the mechanisms of sensitivity and resistance, e.g., by the determination of the reversion of BRCA mutations. Perspective studies are needed to test whether the application of liquid biopsy will significantly improve HGS-EOC management and patients' survival.
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Affiliation(s)
- Lara Paracchini
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy;
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Maurizio D’Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
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Wallander K, Eisfeldt J, Lindblad M, Nilsson D, Billiau K, Foroughi H, Nordenskjöld M, Liedén A, Tham E. Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients. PLoS One 2021; 16:e0245488. [PMID: 33539436 PMCID: PMC7861431 DOI: 10.1371/journal.pone.0245488] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/30/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Analysis of cell-free tumour DNA, a liquid biopsy, is a promising biomarker for cancer. We have performed a proof-of principle study to test the applicability in the clinical setting, analysing copy number alterations (CNAs) in plasma and tumour tissue from 44 patients with gastro-oesophageal cancer. METHODS DNA was isolated from blood plasma and a tissue sample from each patient. Array-CGH was applied to the tissue DNA. The cell-free plasma DNA was sequenced by low-coverage whole-genome sequencing using a clinical pipeline for non-invasive prenatal testing. WISECONDOR and ichorCNA, two bioinformatic tools, were used to process the output data and were compared to each other. RESULTS Cancer-associated CNAs could be seen in 59% (26/44) of the tissue biopsies. In the plasma samples, a targeted approach analysing 61 regions of special interest in gastro-oesophageal cancer detected cancer-associated CNAs with a z-score >5 in 11 patients. Broadening the analysis to a whole-genome view, 17/44 patients (39%) had cancer-associated CNAs using WISECONDOR and 13 (30%) using ichorCNA. Of the 26 patients with tissue-verified cancer-associated CNAs, 14 (54%) had corresponding CNAs in plasma. Potentially clinically actionable amplifications overlapping the genes VEGFA, EGFR and FGFR2 were detected in the plasma from three patients. CONCLUSIONS We conclude that low-coverage whole-genome sequencing without prior knowledge of the tumour alterations could become a useful tool for cell-free tumour DNA analysis of total CNAs in plasma from patients with gastro-oesophageal cancer.
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Affiliation(s)
- Karin Wallander
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mats Lindblad
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Upper Abdominal Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Kenny Billiau
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hassan Foroughi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Agne Liedén
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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12
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Openshaw MR, Suwaidan AA, Ottolini B, Fernandez-Garcia D, Richards CJ, Page K, Guttery DS, Thomas AL, Shaw JA. Longitudinal monitoring of circulating tumour DNA improves prognostication and relapse detection in gastroesophageal adenocarcinoma. Br J Cancer 2020; 123:1271-1279. [PMID: 32719550 PMCID: PMC7555811 DOI: 10.1038/s41416-020-1002-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gastroesophageal adenocarcinoma (GOA) has poor clinical outcomes and lacks reliable blood markers. Here we present circulating tumour DNA (ctDNA) as an emerging biomarker. METHODS Forty patients (17 palliative and 23 curative) were followed by serial plasma monitoring. Primary tumour DNA was analysed by targeted next-generation sequencing to identify somatic single-nucleotide variants (SNVs), and Nanostring nCounter® to detect copy number alterations (CNAs). Patient-specific SNVs and CNA amplifications (CNAamp) were analysed in plasma using digital droplet PCR and quantitative PCR, respectively. RESULTS Thirty-five patients (13 palliative, 22 curative) had ≥1 SNVs and/or CNAamp detected in primary tumour DNA suitable for tracking in plasma. Eighteen of 35 patients (nine palliative, nine curative) had ≥1 ctDNA-positive plasma sample. Detection of postoperative ctDNA predicted short RFS (190 vs 934 days, HR = 3.7, p = 0.028) and subsequent relapse (PPV for relapse 0.83). High ctDNA levels (>60.5 copies/ml) at diagnosis of metastatic disease predicted poor OS (90 vs 372 days, HR = 11.7 p < 0.001). CONCLUSION Sensitive ctDNA detection allows disease monitoring and prediction of short OS in metastatic patients. Presence of ctDNA postoperatively predicts relapse and defines a 'molecular relapse' before overt clinical disease. This lead time defines a potential therapeutic window for additional anticancer therapy.
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Affiliation(s)
- Mark R Openshaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
| | | | - Barbara Ottolini
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | | | - Cathy J Richards
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Karen Page
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Anne L Thomas
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Jacqui A Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
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Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Mol Biol Evol 2020; 37:320-326. [PMID: 31642480 PMCID: PMC6993850 DOI: 10.1093/molbev/msz242] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understanding of the underlying molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways. We also highlight current challenges to applying these concepts, and propose ways in which incorporating these concepts could identify new therapeutic modes and vulnerabilities in cancer.
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Affiliation(s)
- Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Heather Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, MA
| | | | - Ella F Gunady
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Amy M Boddy
- Department of Anthropology, University of California, Santa Barbara, CA
| | | | | | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | | | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom
- King’s College London, London, United Kingdom
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Kate Megquier
- Broad Institute, Massachusettes Institute of Technology and Harvard University
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, and Department of Biology, Temple University, Philadelphia, PA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
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