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Tivey A, Lee RJ, Clipson A, Hill SM, Lorigan P, Rothwell DG, Dive C, Mouliere F. Mining nucleic acid "omics" to boost liquid biopsy in cancer. Cell Rep Med 2024; 5:101736. [PMID: 39293399 DOI: 10.1016/j.xcrm.2024.101736] [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: 04/29/2024] [Revised: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Treatments for cancer patients are becoming increasingly complex, and there is a growing desire from clinicians and patients for biomarkers that can account for this complexity to support informed decisions about clinical care. To achieve precision medicine, the new generation of biomarkers must reflect the spatial and temporal heterogeneity of cancer biology both between patients and within an individual patient. Mining the different layers of 'omics in a multi-modal way from a minimally invasive, easily repeatable, liquid biopsy has increasing potential in a range of clinical applications, and for improving our understanding of treatment response and resistance. Here, we detail the recent developments and methods allowing exploration of genomic, epigenomic, transcriptomic, and fragmentomic layers of 'omics from liquid biopsy, and their integration in a range of applications. We also consider the specific challenges that are posed by the clinical implementation of multi-omic liquid biopsies.
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Affiliation(s)
- Ann Tivey
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK; Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rebecca J Lee
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK; Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Alexandra Clipson
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Steven M Hill
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Paul Lorigan
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Dominic G Rothwell
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
| | - Florent Mouliere
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK.
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2
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Egger ME, Alexander E, Van Meter T, Kong M, Maung AA, Valdes R, Hall MB, Linder MW. Corresponding ctDNA and tumor burden dynamics in metastatic melanoma patients on systemic treatment. Transl Oncol 2024; 42:101883. [PMID: 38306914 PMCID: PMC10850110 DOI: 10.1016/j.tranon.2024.101883] [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: 04/13/2023] [Revised: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Radiographic imaging is the current standard for monitoring progression of tumor-burden and therapeutic resistance in patients with metastatic melanoma. Plasma circulating tumor DNA (ctDNA) has shown promise as a survelience tool, but longitudinal data on the dynamics between plasma ctDNA concentrations and radiographic imaging is lacking. We evaluated the relationship between longitudinal radiographic measures of tumor burden and ctDNA concentrations in plasma on 30 patients with metastatic melanoma on systemic treatment. In 9 patients with no radiographic evidence of disease over a total of 15 time points, ctDNA concentrations were undetectable. In 21 patients with radiographic tumor burden, ctDNA was detected in 81 % of 58 time points. Plasma ctDNA concentrations demonstrated a modest positive correlation with total tumor burden (TTB) measurements (R2= 0.49, p < 0.001), with the greatest degree of correlation observed under conditions of progressive disease (PD) (R2 = 0.91, p = 0.032). Plasma ctDNA concentrations were significantly greater at times of RECIST v1.1 progression (PD; 22.1 % ± 5.7 %) when compared to samples collected during stable disease (SD; 4.99 % ± 3.0 %) (p = 0.012); this difference was independent of total tumor burden (p = 0.997). Changes in plasma ctDNA showed a strong correlation with changes in TTB (R2= 0.88, p<0.001). These data suggest that measurements of plasma ctDNA during therapy are a better surrogate for responding versus non-responding disease compared to absolute tumor burden.
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Affiliation(s)
- Michael E Egger
- Department of Surgery, Division of Surgical Oncology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Evan Alexander
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Tracy Van Meter
- Department of Radiology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Maiying Kong
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, Louisville, KY, USA; Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
| | - Aye Aye Maung
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, Louisville, KY, USA; Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
| | - Roland Valdes
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA; Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa Barousse Hall
- UofL Health Brown Cancer Center, Louisville, KY, USA; Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA; UofL Health Brown Cancer Center, Louisville, KY, USA.
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3
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Liu Q, Jiang X, Tu W, Liu L, Huang Y, Xia Y, Xia X, Shi Y. Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review). Exp Ther Med 2024; 27:149. [PMID: 38476918 PMCID: PMC10928970 DOI: 10.3892/etm.2024.12437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) encodes a serine-threonine kinase. The V600E point mutation in the BRAF gene is the most common mutation, predominantly occurring in melanoma, and colorectal, thyroid and non-small cell lung cancer. Particularly in the context of thyroid cancer research, it is routinely employed as a molecular biomarker to assist in diagnosing and predicting the prognosis of papillary thyroid cancer (PTC), and to formulate targeted therapeutic strategies. Currently, several methods are utilized in clinical settings to detect BRAF V600E mutations in patients with PTC. However, the sensitivity and specificity of various detection techniques vary significantly, resulting in diverse detection outcomes. The present review highlights the advantages and disadvantages of the methods currently employed in medical practice, with the aim of guiding clinicians and researchers in selecting the most suitable detection approach for its high sensitivity, reproducibility and potential to develop targeted therapeutic regimens for patients with BRAF gene mutation-associated PTC.
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Affiliation(s)
- Qian Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Lina Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Ying Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuxiao Xia
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xuliang Xia
- Department of General Surgery, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
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Wang K, Lin X, Zhang M, Yang M, Shi X, Xie M, Luo Y. ACEK Biosensor for the Minute-Scale Quantification of Breast Cancer ctDNA. SENSORS (BASEL, SWITZERLAND) 2024; 24:547. [PMID: 38257640 PMCID: PMC10818266 DOI: 10.3390/s24020547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Circulating tumor DNA (ctDNA) appears as a valuable liquid biopsy biomarker in the early diagnosis, treatment, and prognosis of cancer. Here, a biosensing method derived from the AC electrokinetics (ACEK) effect was constructed in this study for the simple, efficient, and rapid method of detection of ctDNA. In the proof-of-concept experiment, ctDNA from the PIK3CA E542K mutant in breast cancer was quantified by detecting a normalized capacitance change rate using a forked-finger gold electrode as the sensing electrode in combination with the ACEK effect. We compared two formats for the construction of the approach by employing varied immobilization strategies; one is to immobilize the DNA capture probe on the electrode surface by Au-S bonding, while the other immobilizes the probe on a self-assembled membrane on the electrode surface by amide bonding. Both formats demonstrated ultrafast detection speed by completing the ctDNA quantification within 1 min and a linear range of 10 fM-10 pM was observed. Meanwhile, the immobilization via the self-assembled membrane yielded improved stability, sensitivity, and specificity than its Au-S bonding counterpart. A detection limit of 1.94 fM was eventually achieved using the optimized approach. This research provides a label-free and minute-scale universal method for the detection of various malignant tumors. The ctDNA biosensors based on the ACEK effect improved according to the probe type or electrode structure and have potential applications in tumor drug efficacy prediction, drug resistance monitoring, screening of high-risk groups, differential diagnosis, monitoring of tiny residual lesions, and prognosis determination.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Maoxiao Zhang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Mengjie Yang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Xiang Shi
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Mingna Xie
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, NHC Key Laboratory of Birth Defects and Reproductive Health, School of Medicine, Chongqing University, Chongqing 400044, China
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Lygre KB, Forthun RB, Høysæter T, Hjelle SM, Eide GE, Gjertsen BT, Pfeffer F, Hovland R. Assessment of postoperative circulating tumour DNA to predict early recurrence in patients with stage I-III right-sided colon cancer: prospective observational study. BJS Open 2024; 8:zrad146. [PMID: 38242575 PMCID: PMC10799327 DOI: 10.1093/bjsopen/zrad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Right-sided colon cancer (RCC) differs in mutation profile and risk of recurrence compared to distal colon cancer. Circulating tumour DNA (ctDNA) present after surgery can identify patients with residual disease after curative surgery and predict risk of early recurrence. METHODS This is a prospective observational biomarker trial with exploration of ctDNA in 50 non-metastatic RCC patients for which oncological right-sided colectomy was performed. Blood samples were collected preoperatively, within 1 month post surgery, 3 months (not mandatory), 6 months and every 6 months thereafter. Plasma cell free DNA and/or tumour was investigated for cancer-related mutations by the next-generation sequencing (NGS) panel AVENIO surveillance specifically designed for ctDNA analysis. Detected mutations were quantified using digital droplet PCR (ddPCR) for follow-up. Recurrence-free survival was explored. RESULTS 50 patients were recruited. Somatic cancer-related mutations were detected in 47/50 patients. ddPCR validated results from NGS for 27/34 (plasma) and 72/72 samples (tumour). Preoperative ctDNA was detected in 31/47 of the stage I/III patients and the majority of ctDNA positive patients showed reduction of ctDNA after surgery (27/31). ctDNA-positive patients at first postoperative sample had high recurrence risk compared to patients without measurable ctDNA (adjusted hazard ratio: 172.91; 95% c.i.: 8.70 to 3437.24; P: 0.001). CONCLUSION ctDNA was detectable in most patients with non-metastatic RCC before surgery. Positive postoperative ctDNA was strongly associated with early recurrence. Detectable postoperative ctDNA is a prognostic factor with high (100%) positive predictive value for recurrence in this cohort of non-metastatic RCC. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov ID: NCT03776591.
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Affiliation(s)
- Kristin B Lygre
- Department of Gastrointestinal Surgery, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Gastrointestinal Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Rakel B Forthun
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
| | - Trude Høysæter
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sigrun M Hjelle
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Geir E Eide
- Centre for Clinical Research, Haukeland University Hospital, Bergen, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Bjørn T Gjertsen
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frank Pfeffer
- Department of Gastrointestinal Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Randi Hovland
- Section for Cancer Genomics, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Biosciences, University of Bergen, Bergen, Norway
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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Geoffrois L, Harlé A, Sahki N, Sikanja A, Granel-Brocard F, Hervieu A, Mortier L, Jeudy G, Michel C, Nardin C, Huin-Schohn C, Merlin JL. Personalized follow-up of circulating DNA in resected stage III/IV melanoma: PERCIMEL multicentric prospective study protocol. BMC Cancer 2023; 23:554. [PMID: 37328818 DOI: 10.1186/s12885-023-11029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND With more than 15,000 new cases /year in France and 2,000 deaths, cutaneous melanoma represents approximately 4% of incidental cancers and 1.2% of cancer related deaths. In locally advanced (stage III) or resectable metastatic (stage IV) melanomas, medical adjuvant treatment is proposed and recent advances had shown the benefit of anti-PD1/PDL1 and anti-CTLA4 immunotherapy as well as anti-BRAF and anti-MEK targeted therapy in BRAF V600 mutated tumors. However, the recurence rate at one year is approximately 30% and justify extensive research of predictive biomarkers. If in metastatic disease, the follow-up of circulating tumor DNA (ctDNA) has been demonstrated, its interest in adjuvant setting remains to be precised, especially because of a lower detection rate. Further, the definition of a molecular response could prove useful to personalized treatment. METHODS PERCIMEL is an open prospective multicentric study executed through collaboration of the Institut de Cancérologie de Lorraine (non-profit comprehensive cancer center) and 6 French university and community hospitals. A total of 165 patients with resected stage III and IV melanoma, eligible to adjuvant imunotherapy or anti-BRAF/MEK kinase inhibitors will be included. The primary endpoint is the presence of ctDNA, 2 to 3 weeks after surgery, defined as mutated ctDNA copy number calculated as the allelic fraction of a clonal mutation relative to total ctDNA. Secondary endpoints are recurrence-free survival, distant metastasis-free survival and specific survival. We will follow ctDNA along treatment, quantitatively through ctDNA mutated copy number variation, qualitatively through the presence of cfDNA and its clonal evolution. Relative and absolute variations of ctDNA during follow-up will be also analyzed. PERCIMEL study aims at provide scientific evidence that ctDNA quantitative and qualitative variations can be used to predict the recurrence of patients with melanoma treated with adjuvant immunotherapy or kinase inhibitors, thus defining the notion of molecular recurrence.
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Affiliation(s)
- Lionnel Geoffrois
- Medical Oncology Department, Institut de Cancérologie de Lorraine, Vandoeuvre Les Nancy, France
| | - Alexandre Harlé
- Biopathology Department, Institut de Cancérologie de Lorraine, CNRS UMR7039 CRAN Université de Lorraine, Vandoeuvre Les Nancy, France
| | - Nassim Sahki
- Methodology Biostatistics Unit, Institut de Cancérologie de Lorraine, Vandoeuvre Les Nancy, France
| | - Aleksandra Sikanja
- Clinical Research Department, Institut de Cancérologie de Lorraine, Vandoeuvre Les Nancy, France
| | | | - Alice Hervieu
- Medical Oncology Department, Centre Georges François Leclerc, Dijon, France
| | - Laurent Mortier
- Dermatology Department CHRU Lille, Inserm U1189, Université de Lille, Lille, France
| | | | - Catherine Michel
- Dermatology Department, GHR Mulhouse Sud Alsace, Mulhouse, France
| | - Charlée Nardin
- Dermatology Department CHU Besançon, Inserm 1098 RIGHT Université Franche Comté, Besançon, France
| | - Cécile Huin-Schohn
- Clinical Research Department, Institut de Cancérologie de Lorraine, Vandoeuvre Les Nancy, France
| | - Jean-Louis Merlin
- Biopathology Department, Institut de Cancérologie de Lorraine, CNRS UMR7039 CRAN Université de Lorraine, Vandoeuvre Les Nancy, France.
- Clinical Research Department, Institut de Cancérologie de Lorraine, Vandoeuvre Les Nancy, France.
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Sestokaite A, Gedvilaite V, Cicenas S, Sabaliauskaite R, Jarmalaite S. Surveillance of cfDNA Hot Spot Mutations in NSCLC Patients during Disease Progression. Int J Mol Sci 2023; 24:ijms24086958. [PMID: 37108122 PMCID: PMC10138687 DOI: 10.3390/ijms24086958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Non-small cell cancer (NSCLC) has been identified with a great variation of mutations that can be surveyed during disease progression. The aim of the study was to identify and monitor lung cancer-specific mutations incidence in cell-free DNA as well as overall plasma cell-free DNA load by means of targeted next-generation sequencing. Sequencing libraries were prepared from cell-free DNA (cfDNA) isolated from 72 plasma samples of 41 patients using the Oncomine Lung cfDNA panel covering hot spot regions of 11 genes. Sequencing was performed with the Ion Torrent™ Ion S5™ system. Four genes were detected with highest mutation incidence: KRAS (43.9% of all cases), followed by ALK (36.6%), TP53 (31.7%), and PIK3CA (29.3%). Seven patients had co-occurring KRAS + TP53 (6/41, 14.6%) or KRAS + PIK3CA (7/41, 17.1%) mutations. Moreover, the mutational status of TP53 as well an overall cell-free DNA load were confirmed to be predictors of poor progression-free survival (HR = 2.5 [0.8-7.7]; p = 0.029 and HR = 2.3 [0.9-5.5]; p = 0.029, respectively) in NSCLC patients. In addition, TP53 mutation status significantly predicts shorter overall survival (HR = 3.4 [1.2-9.7]; p < 0.001). We demonstrated that TP53 mutation incidence as well as a cell-free DNA load can be used as biomarkers for NSCLC monitoring and can help to detect the disease progression prior to radiological confirmation of the status.
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Affiliation(s)
- Agne Sestokaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257 Vilnius, Lithuania
| | - Vaida Gedvilaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
| | - Saulius Cicenas
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
| | | | - Sonata Jarmalaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257 Vilnius, Lithuania
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Buresova M, Benesova L, Minarik M, Ptackova R, Halkova T, Hosek P, Baxa J, Pesek M, Svaton M, Fiala O. Circulating Tumor DNA correlates with Lactate Dehydrogenase, CYFRA 21-1, and CRP levels in patients with advanced NSCLC. J Cancer 2023; 14:1-8. [PMID: 36605490 PMCID: PMC9809334 DOI: 10.7150/jca.78574] [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: 09/01/2022] [Accepted: 10/17/2022] [Indexed: 01/04/2023] Open
Abstract
Purpose: To investigate potential association between selected tumor markers and laboratory parameters (lactate dehydrogenase [LDH], neutrophils, hemoglobin, neutrophils, lymphocytes, C-reactive protein, albumin, carcinoembryonic antigen, and cytokeratin 19 fragment 21-1 [CYFRA 21-1]) and circulating tumor DNA (ctDNA) with survival in patients with advanced non-small cell lung cancer (NSCLC). Patients and Methods: The study encompassed 82 patients from a single center. All patients had (localy-) advanced adenocarcinomas. ctDNA was determined before starting therapy and at 6 weeks follow-up. Laboratory parameters were measured before each cycle of therapy and oncomarkers before starting the therapy as standard clinical practice. Mann-Whitney U test, Cox proportional hazards model, Fisher's exact test, and Kaplan-Meier survival estimation with Gehan-Wilcoxon test were used for statistical analysis of the corresponding variables. Results: We have confirmed predictive or prognostic significance for some of the selected laboratory markers and oncomarkers. Above all, we demonstrate a significant relationship between the levels of LDH and the oncomarker CYFRA 21-1 and the presence or absence of ctDNA at the time of diagnosis. We also demonstrate significantly lower CRP levels in patients within whom the ctDNA disappeared during treatment. A similar but statistically insignificant trend was observed for LDH. Conclusions: CYFRA 21-1, LDH and probably CRP correlate with ctDNA levels in NSCLC. Repeated measurement of these markers could thus help in early detection of disease progression in the same way as does ctDNA monitoring.
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Affiliation(s)
- Marcela Buresova
- Department of Pneumology and Phthisiology, Charles University, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Lucie Benesova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Drnovská 1112/60, Prague, Czech Republic
| | - Marek Minarik
- Elphogene, Drnovská 1112/60, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague, Czech Republic
| | - Renata Ptackova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Drnovská 1112/60, Prague, Czech Republic
| | - Tereza Halkova
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Drnovská 1112/60, Prague, Czech Republic
| | - Petr Hosek
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, Pilsen, Czech Republic
| | - Jan Baxa
- Department of Imaging Methods, Faculty of Medicine and University Hospital in Pilsen, Charles University, alej Svobody 80, Pilsen, Czech Republic
| | - Milos Pesek
- Department of Pneumology and Phthisiology, Charles University, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Pilsen, Czech Republic
| | - Martin Svaton
- Department of Pneumology and Phthisiology, Charles University, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Pilsen, Czech Republic.,✉ Corresponding author: Martin Svatoň, MD, PhD. Department of Pneumology and Phthisiology, Charles University, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Edvarda Benese 1128/13, 305 99 Pilsen, Czech Republic. E-mail: . ORCID: 0000-0002-6821-8677
| | - Ondrej Fiala
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, Pilsen, Czech Republic.,Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, alej Svobody 80, Pilsen, Czech Republic
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10
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Mattila KE, Mäkelä S, Kytölä S, Andersson E, Vihinen P, Ramadan S, Skyttä T, Tiainen L, Vuoristo MS, Tyynelä-Korhonen K, Koivunen J, Kohtamäki L, Aittomäki K, Hernberg M. Circulating tumor DNA is a prognostic biomarker in metastatic melanoma patients treated with chemoimmunotherapy and BRAF inhibitor. Acta Oncol 2022; 61:1263-1267. [DOI: 10.1080/0284186x.2022.2137693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Kalle E. Mattila
- Department of Oncology and Radiotherapy, Fican West Cancer Centre, University of Turku and Turku University Hospital, and InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Siru Mäkelä
- Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Soili Kytölä
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Emma Andersson
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Pia Vihinen
- Department of Oncology and Radiotherapy and Fican West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Susan Ramadan
- Department of Oncology and Radiotherapy and Fican West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Tanja Skyttä
- Department of Oncology and Radiotherapy, Tays Cancer Centre, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leena Tiainen
- Department of Oncology and Radiotherapy, Tays Cancer Centre, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Meri-Sisko Vuoristo
- Department of Oncology and Radiotherapy, Tays Cancer Centre, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Jussi Koivunen
- Department of Oncology and Radiotherapy, University of Oulu and Oulu University Hospital, MRC Oulu, Oulu, Finland
| | - Laura Kohtamäki
- Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Micaela Hernberg
- Comprehensive Cancer Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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11
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The Prognostic Value of a Single, Randomly Timed Circulating Tumor DNA Measurement in Patients with Metastatic Melanoma. Cancers (Basel) 2022; 14:cancers14174158. [PMID: 36077695 PMCID: PMC9455041 DOI: 10.3390/cancers14174158] [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: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary In this study, we investigated the associations of circulating tumor DNA (ctDNA), measured at a random time point during the patient’s treatment, with tumor progression and routine blood markers (protein S100, lactate dehydrogenase (LDH), and C-reactive protein (CRP)) in a cohort of patients with metastatic melanoma. Detectable ctDNA was associated with the presence of extracerebral disease, tumor progression, and poorer overall survival (OS). Elevated S100 and CRP was correlated with detectable ctDNA, whereas LDH was not. Our results further support the use of ctDNA in the clinical management of patients with metastatic melanoma. Abstract Melanoma currently lacks validated blood-based biomarkers for monitoring and predicting treatment efficacy. Circulating tumor DNA (ctDNA), originating from tumor cells and detectable in plasma, has emerged as a possible biomarker in patients with metastatic melanoma. In this retrospective, single-center study, we collected 129 plasma samples from 79 patients with stage IIIB–IV melanoma as determined by the American Joint Committee on Cancer (AJCC, 8th edition). For the determination of ctDNA levels, we used eight different assays of droplet digital polymerase chain reaction (ddPCR) to detect the most common hotspot mutations in the BRAF and NRAS genes. The aim of the study was to investigate the association of the detectability of ctDNA at a non-prespecified time point in a patient’s treatment with tumor progression, and to correlate ctDNA with commonly used biomarkers (protein S100, LDH, and CRP). Patients with detectable ctDNA progressed more frequently in PET-CT within 12 months than those without detectable ctDNA. Detectability of ctDNA was associated with shorter OS in univariate and multivariate analyses. ctDNA was detectable in a statistically significantly larger proportion of patients with distant metastases (79%) than in patients with no distant metastases or only intracranial metastases (32%). Elevated protein S100 and CRP correlated better with detectable ctDNA than LDH. This study supports the potential of ctDNA as a prognostic biomarker in patients with metastatic melanoma. However, additional prospective longitudinal studies with quantitative assessments of ctDNA are necessary to investigate the limitations and strengths of ctDNA as a biomarker.
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12
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Electrochemical Biosensors for Circulating Tumor DNA Detection. BIOSENSORS 2022; 12:bios12080649. [PMID: 36005048 PMCID: PMC9406149 DOI: 10.3390/bios12080649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022]
Abstract
Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.
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13
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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14
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Promising Blood-Based Biomarkers for Melanoma: Recent Progress of Liquid Biopsy and Its Future Perspectives. Curr Treat Options Oncol 2022; 23:562-577. [PMID: 35298769 DOI: 10.1007/s11864-022-00948-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/11/2022]
Abstract
OPINION STATEMENT Because the recent success of novel therapeutic approaches has dramatically changed the clinical management of melanoma, less invasive and repeatable monitoring tools that can predict the disease status, drug resistance, and the development of side effects are increasingly needed. As liquid biopsy has enabled us to diagnose and monitor disease status less invasively, substantial attention has been directed toward this technique, which is gaining importance as a diagnostic and/or prognostic tool. It is evident that microRNA, cell-free DNA, and circulating tumor cells obtained via liquid biopsy are promising diagnostic and prognostic tools for melanoma, and they also have utility for monitoring the disease status and predicting drug effects. Although current challenges exist for each biomarker, such as poor sensitivity and/or specificity and technical problems, recent technical advances have increasingly improved these aspects. For example, next-generation sequencing technology for detecting microRNAs or cell-free DNA enabled high-throughput analysis and provided significantly higher sensitivity. In particular, cancer personalized profiling by deep sequencing for quantifying cell-free DNA is a promising method for high-throughput analysis that provides real-time comprehensive data for patients at various disease stages. For wide clinical implementation, it is necessary to increase the sensitivity for the markers and standardize the assay procedures to make them reproducible, valid, and inexpensive; however, the broad clinical application of liquid biopsy could occur quickly. This review focuses on the significance of liquid biopsy, particularly related to the use of blood samples from patients with melanoma, and discusses its future perspectives.
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15
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Gouda MA, Polivka J, Huang HJ, Treskova I, Pivovarcikova K, Fikrle T, Woznica V, Dustin DJ, Call SG, Meric-Bernstam F, Pesta M, Janku F. Ultrasensitive detection of BRAF mutations in circulating tumor DNA of non-metastatic melanoma. ESMO Open 2022; 7:100357. [PMID: 34942440 PMCID: PMC8695283 DOI: 10.1016/j.esmoop.2021.100357] [Citation(s) in RCA: 8] [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: 10/11/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 12/21/2022] Open
Abstract
Background Implementation of adjuvant therapies in non-metastatic melanoma improved treatment outcomes in some patients; however, adjuvant therapy can be associated with significant cost and risk of toxicity. Therefore, there is an unmet need to better identify patients at high risk of recurrence. Patients and methods We carried out an ultrasensitive droplet digital PCR (ddPCR)-based detection of BRAFV600E-mutated circulating tumor DNA (ctDNA) from blood samples prospectively collected before surgery, 1 hour after surgery, and then serially during follow-up. Results In 80 patients (stages ≤III), BRAFV600E mutations were detected in 47.2% of tissue, in 37.7% of ctDNA samples collected before surgery, and in 25.9% of ctDNA samples collected 1 hour after surgery. Patients with detected ctDNA in blood collected 1 hour after surgery compared to patients without detected ctDNA had higher likelihood of melanoma recurrence (P < 0.001) and shorter median disease-free survival (P = 0.001) and overall survival (P = 0.003). Conclusions Ultrasensitive ddPCR can detect ctDNA in pre- and post-surgical blood samples from patients with resectable melanoma. Detection of ctDNA in post-surgical samples is associated with inferior treatment outcomes. Ultrasensitive ddPCR can detect ctDNA in pre- and post-surgical samples. Detection of ctDNA 1 hour after surgery is associated with inferior treatment outcomes. There were no associations between ctDNA detection at other timepoints and clinical outcomes.
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Affiliation(s)
- M A Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Polivka
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Neurology, University Hospital Pilsen, Pilsen, Czech Republic
| | - H J Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I Treskova
- Department of Plastic Surgery, University Hospital Pilsen, Pilsen, Czech Republic
| | - K Pivovarcikova
- Department of Pathology, University Hospital Pilsen, Pilsen, Czech Republic
| | - T Fikrle
- Department of Dermatovenerology, University Hospital Pilsen, Pilsen, Czech Republic
| | - V Woznica
- Department of Plastic Surgery, University Hospital Pilsen, Pilsen, Czech Republic
| | - D J Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S G Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M Pesta
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - F Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA.
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16
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Henriksen TV, Drue SO, Frydendahl A, Demuth C, Rasmussen MH, Reinert T, Pedersen JS, Andersen CL. Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR. Clin Chem 2022; 68:657-667. [PMID: 35030248 DOI: 10.1093/clinchem/hvab274] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller. METHODS We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods. RESULTS For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty. CONCLUSIONS Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.
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Affiliation(s)
- Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Simon O Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jakob S Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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17
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Domogala DD, Gambin T, Zemet R, Wu CW, Schulze KV, Yang Y, Wilson TA, Machol I, Liu P, Stankiewicz P. Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset. Hum Genomics 2021; 15:72. [PMID: 34930489 PMCID: PMC8686574 DOI: 10.1186/s40246-021-00369-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. METHODS Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). RESULTS In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. CONCLUSIONS Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.
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Affiliation(s)
- Daniel D Domogala
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas at MD Anderson, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chung Wah Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- AiLife Diagnostics, 1920 Country Place Pkwy Suite 100, Pearland, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Baylor Genetics, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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18
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Gracie L, Pan Y, Atenafu EG, Ward DG, Teng M, Pallan L, Stevens NM, Khoja L. Circulating tumour DNA (ctDNA) in metastatic melanoma, a systematic review and meta-analysis. Eur J Cancer 2021; 158:191-207. [PMID: 34757258 DOI: 10.1016/j.ejca.2021.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/31/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Circulating tumour DNA (ctDNA) is an emerging biomarker in melanoma. We performed a systematic review and meta-analysis to explore its clinical utility as a prognostic, pharmacodynamic (PD) and predictive biomarker. METHODS A systematic search was conducted from Jan 2015 to April 2021, of the electronic databases PubMed, Cochrane Library and Ovid MEDLINE to identify studies. Studies were restricted to those published in English within the last 5 years, evaluating ctDNA in humans in ≥10 patients. Survival data were extracted for meta-analysis using pooled treatment effect (TE), i.e. log hazard ratios (HRs) and corresponding standard error of TE for progression-free survival or overall survival differences in patients who were ctDNA positive or negative. PRISMA statement guidelines were followed. RESULTS A meta-analysis of 19 studies grouped according to methodology of ctDNA detection, revealed a combined estimate for HR of progression-free survival (13 studies using droplet digital Polymerase Chain Reaction (ddPCR) methodology (N = 1002) of 2.10 (95% CI: 1.71-2.59) revealing a poorer prognosis when ctDNA was detected. This result was confirmed in the smaller analysis of (non-ddPCR, N = 347) five studies: HR = 2.45 (95% CI: 1.29-4.63). Similar findings were found in the overall survival analysis of nine studies (ddPCR methodology, N = 841) where the combined HR was 2.78 (95% CI: 2.21-3.49) and of the five studies (non-ddPCR methodology, N = 326) where the combined HR was 2.58 (95% CI: 1.74-3.84). Serial ctDNA levels on treatment showed a pharmacodynamic role reflecting response or resistance earlier than radiological assessment. CONCLUSIONS Circulating tumour DNA is a predictive, prognostic and PD biomarker in melanoma. Technical standardisation of assays is required before clinical adoption.
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Affiliation(s)
- Lara Gracie
- College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yi Pan
- Centre for Computational Biology and Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eshetu G Atenafu
- Biostatistics Department, Princess Margaret Cancer Center, University Health Network, University Way, Toronto, Ontario, Canada
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mabel Teng
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Department of Oncology, Birmingham B15 2TH, UK
| | - Lallit Pallan
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Department of Oncology, Birmingham B15 2TH, UK
| | - Neil M Stevens
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Leila Khoja
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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19
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Kamińska P, Buszka K, Zabel M, Nowicki M, Alix-Panabières C, Budna-Tukan J. Liquid Biopsy in Melanoma: Significance in Diagnostics, Prediction and Treatment Monitoring. Int J Mol Sci 2021; 22:9714. [PMID: 34575876 PMCID: PMC8468624 DOI: 10.3390/ijms22189714] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is a common term referring to circulating tumor cells and other biomarkers, such as circulating tumor DNA (ctDNA) or extracellular vesicles. Liquid biopsy presents a range of clinical advantages, such as the low invasiveness of the blood sample collection and continuous control of the tumor progression. In addition, this approach enables the mechanisms of drug resistance to be determined in various methods of cancer treatment, including immunotherapy. However, in the case of melanoma, the application of liquid biopsy in patient stratification and therapy needs further investigation. This review attempts to collect all of the relevant and recent information about circulating melanoma cells (CMCs) related to the context of malignant melanoma and immunotherapy. Furthermore, the biology of liquid biopsy analytes, including CMCs, ctDNA, mRNA and exosomes, as well as techniques for their detection and isolation, are also described. The available data support the notion that thoughtful selection of biomarkers and technologies for their detection can contribute to the development of precision medicine by increasing the efficacy of cancer diagnostics and treatment.
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Affiliation(s)
- Paula Kamińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Karolina Buszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Maciej Zabel
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, 65-046 Zielona Góra, Poland;
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 34093 Montpellier, France;
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
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20
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Hallermayr A, Benet-Pagès A, Steinke-Lange V, Mansmann U, Rentsch M, Holinski-Feder E, Pickl JMA. Liquid Biopsy Hotspot Variant Assays: Analytical Validation for Application in Residual Disease Detection and Treatment Monitoring. Clin Chem 2021; 67:1483-1491. [PMID: 34392332 DOI: 10.1093/clinchem/hvab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Analysis of circulating tumor DNA (ctDNA) in plasma is a powerful approach to guide decisions in personalized cancer treatment. Given the low concentration of ctDNA in plasma, highly sensitive methods are required to reliably identify clinically relevant variants. METHODS We evaluated the suitability of 5 droplet digital PCR (ddPCR) assays targeting KRAS, BRAF, and EGFR variants for ctDNA analysis in clinical use. RESULTS We investigated assay performance characteristics for very low amounts of variants, showing that the assays had very low limits of blank (0% to 0.11% variant allele frequency, VAF) and limits of quantification (0.41% to 0.7% VAF). Nevertheless, striking differences in detection and quantification of low mutant VAFs between the 5 tested assays were observed, highlighting the need for assay-specific analytical validation. Besides in-depth evaluation, a guide for clinical interpretation of obtained VAFs in plasma was developed, depending on the limits of blank and limits of quantification values. CONCLUSION It is possible to provide comprehensive clinical reports on actionable variants, allowing minimal residual disease detection and treatment monitoring in liquid biopsy.
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Affiliation(s)
- Ariane Hallermayr
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Pettenkofer School of Public Health, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Anna Benet-Pagès
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Markus Rentsch
- Department of General, Visceral and Thorax Surgery, Klinikum Ingolstadt, Germany.,Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University of Munich, Campus Großhadern, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Julia M A Pickl
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
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21
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Tolmeijer SH, Koornstra RHT, de Groot JWB, Geerlings MJ, van Rens DH, Boers-Sonderen MJ, Schalken JA, Gerritsen WR, Ligtenberg MJL, Mehra N. Plasma BRAF Mutation Detection for the Diagnostic and Monitoring Trajectory of Patients with LDH-High Stage IV Melanoma. Cancers (Basel) 2021; 13:3913. [PMID: 34359813 PMCID: PMC8345527 DOI: 10.3390/cancers13153913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 01/16/2023] Open
Abstract
For patients with newly diagnosed metastatic melanoma, rapid BRAF mutation (mBRAF) assessment is vital to promptly initiate systemic therapy. Additionally, blood-based biomarkers are desired to monitor and predict treatment response. Circulating tumor DNA (ctDNA) has shown great promise for minimally invasive mBRAF assessment and treatment monitoring, but validation studies are needed. This prospective study utilized longitudinal plasma samples at regular timepoints (0, 6, 12, 18 weeks) to address the clinical validity of ctDNA measurements in stage IV melanoma patients with elevated serum lactate dehydrogenase (LDH > 250U/L) starting first-line systemic treatment. Using droplet digital PCR, the plasma mBRAF abundance was assessed in 53 patients with a BRAFV600 tissue mutation. Plasma mBRAF was detected in 50/51 patients at baseline (98% sensitivity; median fraction abundance of 19.5%) and 0/17 controls (100% specificity). Patients in whom plasma mBRAF became undetectable during the first 12-18 weeks of treatment had a longer progression-free survival (30.2 vs. 4.0 months; p < 0.001) and cancer-specific survival (not reached vs. 10.2 months; p < 0.001) compared to patients with detectable mBRAF. The ctDNA dynamics outperformed LDH and S100 dynamics. These results confirm the clinical validity of ctDNA measurements as a minimally invasive biomarker for the diagnostic and monitoring trajectory of patients with LDH-high stage IV melanoma.
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Affiliation(s)
- Sofie H. Tolmeijer
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Rutger H. T. Koornstra
- Department of Medical Oncology, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.H.T.K.); (D.H.v.R.); (M.J.B.-S.); (W.R.G.)
- Department of Medical Oncology, Rijnstate Hospital, 6815 AD Arnhem, The Netherlands
| | | | - Maartje J. Geerlings
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (M.J.G.); (M.J.L.L.)
| | - Dirk H. van Rens
- Department of Medical Oncology, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.H.T.K.); (D.H.v.R.); (M.J.B.-S.); (W.R.G.)
| | - Marye J. Boers-Sonderen
- Department of Medical Oncology, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.H.T.K.); (D.H.v.R.); (M.J.B.-S.); (W.R.G.)
| | - Jack A. Schalken
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Winald R. Gerritsen
- Department of Medical Oncology, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.H.T.K.); (D.H.v.R.); (M.J.B.-S.); (W.R.G.)
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (M.J.G.); (M.J.L.L.)
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.H.T.K.); (D.H.v.R.); (M.J.B.-S.); (W.R.G.)
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22
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Feng SN, Cen XT, Tan R, Wei SS, Sun LD. The prognostic value of circulating tumor DNA in patients with melanoma: A systematic review and meta-analysis. Transl Oncol 2021; 14:101072. [PMID: 33744725 PMCID: PMC7985561 DOI: 10.1016/j.tranon.2021.101072] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has been investigated as a potential prognostic biomarker to evaluate the therapeutic efficacy and disease progression in melanoma patients, yet results remain inconclusive. The purpose of this study was to illustrate the prognostic value of ctDNA in melanoma. OBJECTIVES To describe the clinical prognostic value of ctDNA for melanoma patients. METHODS Searched for eligible articles from Pubmed, Web of Science and Embase. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated to evaluate the association between ctDNA at baseline or during treatment and overall survival (OS) and progression-free survival (PFS). RESULTS A total of 9 articles were obtained, involving 617 melanoma patients. The pooled HRs revealed that compared with baseline undetectable ctDNA patients, detectable ctDNA was highly correlated with poor OS (HR 2.91, 95% CI: 2.22-3.82; p < 0.001) and PFS (HR 2.75, 95% CI: 1.98-3.83; p < 0.001). A meta-analysis of these adjusted HRs was performed and confirmed that ctDNA collected at baseline was associated with poorer OS/PFS (OS: HR 3.00, 95% CI 2.19-4.11, p < 0.001/PFS: HR 2.68, 95% CI 1.77-4.06, p < 0.001). During treatment, a significant association was shown between ctDNA and poorer OS/PFS (OS: HR 6.26, 95% CI 2.48-15.80, p < 0.001; PFS: HR 4.93, 95% CI 2.36-10.33, p < 0.001). CONCLUSION Investigation and application of ctDNA will improve "liquid biopsy" and play a role in early prediction, monitoring disease progression and precise adjusting treatment strategies in melanoma patients.
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Affiliation(s)
- S N Feng
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - X T Cen
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - R Tan
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - S S Wei
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - L D Sun
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China; Departmet of Dermatology, the Fifth Affiliated Hospital of Southern Medical University, No.566 Congcheng Avenue, Guangzhou, China.
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Content of circulating tumor DNA depends on the tumor type and the dynamics of tumor size, but is not influenced significantly by physical exercise, time of the day or recent meal. Cancer Genet 2021; 256-257:165-178. [PMID: 34186498 DOI: 10.1016/j.cancergen.2021.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 01/20/2023]
Abstract
PURPOSE This study aimed to investigate factors, which influence the content of circulating tumor DNA (ctDNA). METHODS 398 serial plasma samples were collected within 1-7 consecutive days from patients with EGFR-mutated lung cancer (n = 13), RAS/RAF-mutated colorectal cancer (n = 54) and BRAF-mutated melanoma (n = 17), who presented with measurable tumor disease. The amount of ctDNA was determined by ddPCR. RESULTS Among 82 patients, who donated 2-6 serial plasma samples, 42 subjects were classified as ctDNA-positive; only 22% cases were mutation-positive across all consecutive tests, while 24/82 (29%) patients showed presence of mutated ctDNA in some but not all blood draws. Subjects with progressing tumors had higher probability of being detected ctDNA-positive as compared to patients, who responded to therapy or had stable disease (39/55 (71%) vs. 4/24 (17%); p = 0.0001). Our study failed to reveal the impact of the time of the day, recent meal or prior physical exercise on the results of ctDNA testing. CONCLUSIONS Presence of ctDNA in plasma is particularly characteristic for patients, who experience clinical progression of tumor disease. Consecutive plasma tests may occasionally provide discordant data; thus, the repetition of analysis may be advised in certain cases in order to ensure the validity of negative ctDNA result.
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Zheng Y, Sun H, Cong L, Liu C, Sun Q, Wu N, Cong X. Prognostic Value of ctDNA Mutation in Melanoma: A Meta-Analysis. JOURNAL OF ONCOLOGY 2021; 2021:6660571. [PMID: 34035810 PMCID: PMC8116156 DOI: 10.1155/2021/6660571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/18/2021] [Accepted: 03/26/2021] [Indexed: 01/11/2023]
Abstract
PURPOSE Melanoma is the most aggressive form of skin cancer. Circulating tumor DNA (ctDNA) is a diagnostic and prognostic marker of melanoma. However, whether ctDNA mutations can independently predict survival remains controversial. This meta-analysis assessed the prognostic value of the presence or change in ctDNA mutations in melanoma patients. METHODS We identified studies from the PubMed, EMBASE, Web of Science, and Cochrane databases. We estimated the combined hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS) using either fixed-effect or random-effect models based on heterogeneity. RESULTS Sixteen studies including 1,781 patients were included. Both baseline and posttreatment detectable ctDNA were associated with poor OS (baseline detectable vs. undetectable, pooled HR = 1.97, 95% CI = 1.64-2.36, P < 0.00001; baseline undetectable vs. detectable, pooled HR = 0.19, 95% CI = 0.11-0.36, P < 0.00001; posttreatment detectable vs. undetectable, pooled HR = 2.36, 95% CI = 1.30-4.28, P=0.005). For PFS, baseline detectable ctDNA may be associated with adverse PFS (baseline detectable vs. undetectable, pooled HR = 1.41, 95% CI = 0.84-2.37, P=0.19; baseline undetectable vs. detectable, pooled HR = 0.43, 95% CI = 0.19-0.95, P=0.04) and baseline high ctDNA and increased ctDNA were significantly associated with adverse PFS (baseline high vs. low/undetectable, pooled HR = 3.29, 95% CI = 1.73-6.25, P=0.0003; increase vs. decrease, pooled HR = 4.48, 95% CI = 2.45-8.17, P < 0.00001). The baseline BRAFV600 ctDNA mutation-positive group was significantly associated with adverse OS compared with the baseline ctDNA-negative group (pooled HR = 1.90, 95% CI = 1.58-2.29, P < 0.00001). There were no significant differences in PFS between the baseline BRAFV600 ctDNA mutation-detectable group and the undetectable group (pooled HR = 1.02, 95% CI = 0.72-1.44, P=0.92). CONCLUSION The presence or elevation of ctDNA mutation or BRAFV600 ctDNA mutation was significantly associated with worse prognosis in melanoma patients.
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Affiliation(s)
- Yang Zheng
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hongyan Sun
- Biobank, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lele Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chenlu Liu
- Biobank, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qian Sun
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Nan Wu
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xianling Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
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Bunda S, Zuccato JA, Voisin MR, Wang JZ, Nassiri F, Patil V, Mansouri S, Zadeh G. Liquid Biomarkers for Improved Diagnosis and Classification of CNS Tumors. Int J Mol Sci 2021; 22:4548. [PMID: 33925295 PMCID: PMC8123653 DOI: 10.3390/ijms22094548] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Liquid biopsy, as a non-invasive technique for cancer diagnosis, has emerged as a major step forward in conquering tumors. Current practice in diagnosis of central nervous system (CNS) tumors involves invasive acquisition of tumor biopsy upon detection of tumor on neuroimaging. Liquid biopsy enables non-invasive, rapid, precise and, in particular, real-time cancer detection, prognosis and treatment monitoring, especially for CNS tumors. This approach can also uncover the heterogeneity of these tumors and will likely replace tissue biopsy in the future. Key components of liquid biopsy mainly include circulating tumor cells (CTC), circulating tumor nucleic acids (ctDNA, miRNA) and exosomes and samples can be obtained from the cerebrospinal fluid, plasma and serum of patients with CNS malignancies. This review covers current progress in application of liquid biopsies for diagnosis and monitoring of CNS malignancies.
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Affiliation(s)
- Severa Bunda
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Jeffrey A. Zuccato
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Mathew R. Voisin
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Justin Z. Wang
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Farshad Nassiri
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Vikas Patil
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Sheila Mansouri
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Gelareh Zadeh
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
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Nordgård O, Brendsdal Forthun R, Lapin M, Grønberg BH, Kalland KH, Kopperud RK, Thomsen LCV, Tjensvoll K, Gilje B, Gjertsen BT, Hovland R. Liquid Biopsies in Solid Cancers: Implementation in a Nordic Healthcare System. Cancers (Basel) 2021; 13:cancers13081861. [PMID: 33924696 PMCID: PMC8069797 DOI: 10.3390/cancers13081861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary We here review liquid biopsy methods and their use in the diagnostics and treatment of patients with solid cancers. More specifically, circulating tumor DNA, circulating tumor cells, and their current and future clinical applications are considered. Important factors for further integration of liquid biopsy methods in clinical practice are discussed, with a special focus on a Nordic Healthcare system. Abstract Liquid biopsies have emerged as a potential new diagnostic tool, providing detailed information relevant for characterization and treatment of solid cancers. We here present an overview of current evidence supporting the clinical relevance of liquid biopsy assessments. We also discuss the implementation of liquid biopsies in clinical studies and their current and future clinical role, with a special reference to the Nordic healthcare systems. Our considerations are restricted to the most established liquid biopsy specimens: circulating tumor DNA (ctDNA) and circulating tumor cells (CTC). Both ctDNA and CTCs have been used for prognostic stratification, treatment choices, and treatment monitoring in solid cancers. Several recent publications also support the role of ctDNA in early cancer detection. ctDNA seems to provide more robust clinically relevant information in general, whereas CTCs have the potential to answer more basic questions related to cancer biology and metastasis. Epidermal growth factor receptor-directed treatment of non-small-cell lung cancer represents a clinical setting where ctDNA already has entered the clinic. The role of liquid biopsies in treatment decisions, standardization of methods, diagnostic performance and the need for further research, as well as cost and regulatory issues were identified as factors that influence further integration in the clinic. In conclusion, substantial evidence supports the clinical utility of liquid biopsies in cancer diagnostics, but further research is still required for a more general application in clinical practice.
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Affiliation(s)
- Oddmund Nordgård
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
- Correspondence:
| | - Rakel Brendsdal Forthun
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway; (R.B.F.); (R.H.)
- Section of Cancer Genomics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Morten Lapin
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- Department of Oncology, St. Olav’s Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Karl Henning Kalland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Reidun Kristin Kopperud
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
| | - Liv Cecilie Vestrheim Thomsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
| | - Kjersti Tjensvoll
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørnar Gilje
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, 5021 Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway; (R.B.F.); (R.H.)
- Section of Cancer Genomics, Haukeland University Hospital, 5021 Bergen, Norway
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Blood-Based Detection of BRAF V600E in Gliomas and Brain Tumor Metastasis. Cancers (Basel) 2021; 13:cancers13061227. [PMID: 33799709 PMCID: PMC7998685 DOI: 10.3390/cancers13061227] [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: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The BRAF V600E mutation has been identified as a key driver in brain tumors and brain tumor metastasis. The ability to detect this mutation in a minimally invasive plasma assay offers advantages over traditional tissue-based biopsy for the disease diagnosis and monitoring. The aim of this study was to develop an assay for the detection of BRAF V600E in the plasma of patients with brain tumors and brain tumor metastasis. We demonstrate BRAF V600E detection using a novel plasma-based ddPCR assay. We detect the mutation in circulating nucleic acids in 4/5 patients with mutant gliomas and metastatic melanoma. We also show correlation between plasma BRAF V600E and clinical status. This proof of principle study is important in the context of application of liquid biopsy in plasma to the neuro-oncologic field. The assay may be useful as a diagnostic adjunct, prognostication tool, and method for monitoring of disease and treatment response. Abstract Liquid biopsy provides a minimally invasive platform for the detection of tumor-derived information, including hotspot mutations, such as BRAF V600E. In this study, we provide evidence of the technical development of a ddPCR assay for the detection of BRAF V600E mutations in the plasma of patients with glioma or brain metastasis. In a small patient cohort (n = 9, n = 5 BRAF V600E, n = 4 BRAF WT, n = 4 healthy control), we were able to detect the BRAF V600E mutation in the plasma of 4/5 patients with BRAF V600E-tissue confirmed mutant tumors, and none of the BRAF WT tumors. We also provide evidence in two metastatic patients with longitudinal monitoring, where the plasma-based BRAF V600E mutation correlated with clinical disease status. This proof of principle study demonstrates the potential of this assay to serve as an adjunctive tool for the detection, monitoring, and molecular characterization of BRAF mutant gliomas and brain metastasis.
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da Costa VR, Bim LV, Pacheco e Silva LDP, Colloza-Gama GA, Bastos AU, Delcelo R, Oler G, Cerutti JM. Advances in Detecting Low Prevalence Somatic TERT Promoter Mutations in Papillary Thyroid Carcinoma. Front Endocrinol (Lausanne) 2021; 12:643151. [PMID: 33776938 PMCID: PMC7994758 DOI: 10.3389/fendo.2021.643151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Two recurrent TERT (telomerase reverse transcriptase) promoter mutations, C228T and C250T, have been reported in thyroid carcinomas and were correlated with high-risk clinicopathological features and a worse prognosis. Although far more frequent in the poorly differentiated and undifferentiated thyroid cancer, the TERT promoter mutations play a significant role on PTC recurrence and disease-specific mortality. However, the prevalence varies considerably through studies and it is uncertain if these differences are due to population variation or the methodology used to detect TERT mutations. In this study we aim to compare three different strategies to detect TERT promoter mutations in PTC. METHODS DNA was isolated from formalin-fixed paraffin-embedded (FFPE) specimens from 89 PTC and 40 paired lymph node metastases. The prevalence of the hot spot TERT C228T and C250T mutations was assessed in FFPE samples using TaqMan SNP genotyping assays. Random samples were tested by Sanger Sequencing and droplet digital PCR (ddPCR). RESULTS In general, 16 out of 89 (18%) PTC samples and 14 out of 40 (35%) lymph node metastases harbored TERT promoter mutations by TaqMan assay. Sanger sequencing, performed in random selected samples, failed to detect TERT mutations in four samples that were positive by TaqMan SNP genotyping assay. Remarkably, ddPCR assay allowed detection of TERT promoter mutations in six samples that harbor very low mutant allele frequency (≤ 2%) and were negative by both genotype assay and Sanger Sequencing. CONCLUSION This study observed a good concordance among the methodologies used to detect TERT promoter mutations when a high percentage of mutated alleles was present. Sanger analysis demonstrated a limit of detection for mutated alleles. Therefore, the prevalence of TERT promoter mutations in PTC may be higher than previously reported, since most studies have conventionally used Sanger sequencing. The efficient characterization of genetic alterations that are used as preoperative or postoperative diagnostic, risk stratification of the patient and individualized treatment decisions, mainly in highly heterogeneous tumors, require highly sensitive and specific approaches.
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Affiliation(s)
- Vitor Rodrigues da Costa
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Larissa Valdemarin Bim
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Gabriel Avelar Colloza-Gama
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - André Uchimura Bastos
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
- Repare DNA Laboratory, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Rosana Delcelo
- Department of Pathology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gisele Oler
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Janete Maria Cerutti,
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Gandini S, Zanna I, De Angelis SP, Cocorocchio E, Queirolo P, Lee JH, Carlino MS, Mazzarella L, Achutti Duso B, Palli D, Raimondi S, Caini S. Circulating tumour DNA and melanoma survival: A systematic literature review and meta-analysis. Crit Rev Oncol Hematol 2020; 157:103187. [PMID: 33276181 DOI: 10.1016/j.critrevonc.2020.103187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
We reviewed and meta-analysed the available evidence (until December 2019) about circulating tumour DNA (ctDNA) levels and melanoma patients survival. We included twenty-six studies (>2000 patients overall), which included mostly stage III-IV cutaneous melanoma patients and differed widely in terms of systemic therapy received and somatic mutations that were searched. Patients with detectable ctDNA before treatment had worse progression-free survival (PFS) (summary hazard ratio (SHR) 2.47, 95 % confidence intervals (CI) 1.85-3.29) and overall survival (OS) (SHR 2.98, 95 % CI 2.26-3.92), with no difference by tumour stage. ctDNA detectability during follow-up was associated with poorer PFS (SHR 4.27, 95 %CI 2.75-6.63) and OS (SHR 3.91, 95 %CI 1.97-7.78); in the latter case, the association was stronger (p = 0.01) for stage IV vs. III melanomas. Between-estimates heterogeneity was low for all pooled estimates. ctDNA is a strong prognostic biomarker for advanced-stage melanoma patients, robust across tumour (e.g. genomic profile) and patients (e.g. systemic therapy) characteristics.
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Affiliation(s)
- Sara Gandini
- Molecular and Pharmaco-Epidemiology Unit Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Ines Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Simone Pietro De Angelis
- Molecular and Pharmaco-Epidemiology Unit Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Emilia Cocorocchio
- Division of Medical Oncology of Melanoma, Sarcoma and Rare Tumors, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Paola Queirolo
- Division of Medical Oncology of Melanoma, Sarcoma and Rare Tumors, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Jenny H Lee
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | - Matteo S Carlino
- Department of Clinical Oncology, Westmead and Blacktown Hospitals, Melanoma Institute of Australia and the University of Sydney, Sydney, Australia
| | - Luca Mazzarella
- Molecular and Pharmaco-Epidemiology Unit Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Bruno Achutti Duso
- Molecular and Pharmaco-Epidemiology Unit Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Domenico Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Sara Raimondi
- Molecular and Pharmaco-Epidemiology Unit Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Saverio Caini
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy.
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Vannas C, Bjursten S, Filges S, Fagman H, Ståhlberg A, Levin M. Dynamic ctDNA evaluation of a patient with BRAFV600E metastatic melanoma demonstrates the utility of ctDNA for disease monitoring and tumor clonality analysis. Acta Oncol 2020; 59:1388-1392. [PMID: 32772605 DOI: 10.1080/0284186x.2020.1802064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- C. Vannas
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Sahlgrenska Cancer Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - S. Bjursten
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S. Filges
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - H. Fagman
- Sahlgrenska Cancer Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - A. Ståhlberg
- Sahlgrenska Cancer Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - M. Levin
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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