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Laven-Law G, Kichenadasse G, Young GP, Symonds EL, Winter JM. BCAT1, IKZF1 and SEPT9: methylated DNA biomarkers for detection of pan-gastrointestinal adenocarcinomas. Biomarkers 2024:1-11. [PMID: 38644767 DOI: 10.1080/1354750x.2024.2340663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
INTRODUCTION Methylated circulating tumour DNA (ctDNA) blood tests for BCAT1/IKZF1 (COLVERA) and SEPT9 (Epi proColon) are used to detect colorectal cancer (CRC). However, there are no ctDNA assays approved for other gastrointestinal adenocarcinomas. We aimed to characterize BCAT1, IKZF1 and SEPT9 methylation in different gastrointestinal adenocarcinoma and non-gastrointestinal tumours to determine if these validated CRC biomarkers might be useful for pan-gastrointestinal adenocarcinoma detection. METHODS Tissue DNA methylation data from colorectal (COAD, READ), gastroesophageal (ESCA, STAD), pancreatic (PAAD) and cholangiocarcinoma (CHOL) adenocarcinoma cohorts within The Cancer Genome Atlas were used for differential methylation analyses. Clinicodemographic predictors of BCAT1, IKZF1 and SEPT9 methylation, and the selectivity of hypermethylated BCAT1, IKZF1 and SEPT9 for colorectal adenocarcinomas in comparison to other cancers were each explored with beta regression. RESULTS Hypermethylated BCAT1, IKZF1 and SEPT9 were each differentially methylated in colorectal and gastroesophageal adenocarcinomas. IKZF1 was differentially methylated in pancreatic adenocarcinoma. Hypermethylated DNA biomarkers BCAT1, IKZF1 and SEPT9 were largely stable across different stages of disease and were highly selective for gastrointestinal adenocarcinomas relative to other cancer types. DISCUSSION Existing CRC methylated ctDNA blood tests for BCAT1/IKZF1 and SEPT9 might be usefully repurposed for use in other gastrointestinal adenocarcinomas and warrant further prospective ctDNA studies.
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Affiliation(s)
- Geraldine Laven-Law
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Graeme P Young
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
| | - Erin L Symonds
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia
| | - Jean M Winter
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Adelaide, South Australia
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Calabretta E, di Trani M, Corrado F, Sollini M, Cristaldi V, Marino F, Terzi di Bergamo L, Bruscaggin A, Pirosa MC, Bramanti S, Chiti A, Rossi D, Carlo-Stella C. Baseline circulating tumour DNA and interim PET predict response in relapsed/refractory classical Hodgkin lymphoma. Br J Haematol 2024; 204:514-524. [PMID: 37853658 DOI: 10.1111/bjh.19162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/06/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
Reliable biomarkers for early identification of treatment failure in relapsed/refractory (r/r) classical Hodgkin lymphoma (cHL) are lacking. Circulating tumour DNA (ctDNA) profiling has emerged as a powerful predictive and prognostic tool in several haemopoietic and non-haemopoietic malignancies and may guide rational treatment choices in r/r cHL. To assess the predictive and prognostic value of ctDNA, we performed a retrospective analysis on 55 r/r cHL patients treated with the bendamustine, gemcitabine and vinorelbine (BEGEV) regimen and additionally evaluated the potential utility of integrating ctDNA with interim [18 F]-FDG positron emission tomography (iPET). Baseline ctDNA genotyping in r/r cHL mirrored gene mutations and pathways involved in newly diagnosed cHL. We found that baseline ctDNA quantification and serial ctDNA monitoring have prognostic value in r/r cHL receiving salvage chemotherapy. Lastly, integrating ctDNA quantification with iPET evaluation may improve the early identification of patients at high risk of failing standard salvage therapy, who may benefit from an early switch to immunotherapeutic agents. Collectively, our results support the implementation of non-invasive methods to detect minimal residual disease in recurrent cHL and justify its prospective evaluation in appropriately designed clinical trials.
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Affiliation(s)
- Eleonora Calabretta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Martina di Trani
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Francesco Corrado
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Martina Sollini
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Nuclear Medicine, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Vanessa Cristaldi
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Fabrizio Marino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Lodovico Terzi di Bergamo
- Laboratory of Experimental Hematology, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Alessio Bruscaggin
- Laboratory of Experimental Hematology, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Maria Cristina Pirosa
- Laboratory of Experimental Hematology, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Stefania Bramanti
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Arturo Chiti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Nuclear Medicine, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Davide Rossi
- Laboratory of Experimental Hematology, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Carmelo Carlo-Stella
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Department of Oncology and Hematology, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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Roque R, Ribeiro IP, Figueiredo-Dias M, Gourley C, Carreira IM. Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer. Biology (Basel) 2024; 13:88. [PMID: 38392306 PMCID: PMC10886635 DOI: 10.3390/biology13020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10-5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.
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Affiliation(s)
- Ricardo Roque
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Portuguese Institute of Oncology of Coimbra, 3000-075 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Margarida Figueiredo-Dias
- Faculty of Medicine, Gynecology Department, University of Coimbra, 3004-504 Coimbra, Portugal
- Coimbra Academic and Clinical Centre, 3000-370 Coimbra, Portugal
- Gynecology Department, Hospital University Centre of Coimbra, 3004-561 Coimbra, Portugal
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
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Dziadziuszko R, Peled N, Mok T, Peters S, Aix SP, Alatorre-Alexander J, Vicuna BD, Maclennan M, Bhagawati-Prasad V, Shagan SM, Schleifman E, Ruf T, Mathisen MS, Gadgeel SM. High-dose alectinib for RET fusion-positive non-small cell lung cancer in the Blood First Assay Screening Trial. Contemp Oncol (Pozn) 2024; 27:217-223. [PMID: 38405208 PMCID: PMC10883190 DOI: 10.5114/wo.2023.135246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/06/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction This paper presents results from Cohort B (rearranged during transfection [RET], fusion-positive) of the Blood First Assay Screening Trial in patients with advanced non-small cell lung cancer (NSCLC) screened for genetic alterations using blood-based next-generation sequencing. Material and methods Adults with advanced RET fusion-positive NSCLC received alectinib 900 mg twice daily (BID) in Phase I. Enrolment closed prematurely with Phase II uninitiated. Results Among eight treated patients, confirmed best overall responses in evaluable patients were stable disease (4/5) and progressive disease (1/5). One dose-limiting toxicity (death, unknown cause) was considered by the investigator to be related to treatment and underlying disease. Serious adverse events (SAEs) occurred in five patients, and SAEs that may be related to treatment occurred in two patients. Conclusions Alectinib showed limited activity in advanced RET fusion-positive NSCLC, and further investigation was not conducted due to the development of selective RET inhibitors pralsetinib and selpercatinib. No new safety signals were observed, and the safety profile of alectinib was in line with previous reports at the 600 mg BID dose.
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Affiliation(s)
- Rafal Dziadziuszko
- Department of Oncology and Radiotherapy and Early Clinical Trials Centre, Medical University of Gdańsk, Gdańsk, Poland
| | - Nir Peled
- Soroka Medical Centre and Ben-Gurion University, Beer-Sheeva, Israel
- Helmsley Cancer Centre, Shaare Zedek Medical Centre, Hebrew University, Jerusalem, Israel (currently)
| | - Tony Mok
- State Key Laboratory of Translational Oncology, Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong
| | - Solange Peters
- Lausanne University Hospital, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | | | | | | | | | | | | | | | | | | | - Shirish M. Gadgeel
- Department of Internal Medicine, Henry Ford Cancer Institute/Henry Ford Health System, Detroit, MI, USA
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Hofman P, Denis MG. The use of minimal residual disease in thoracic oncology: Gaps between promises and the on-the-ground reality of daily practice. Cytopathology 2024; 35:7-15. [PMID: 37222472 DOI: 10.1111/cyt.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
The assessment of minimal residual disease (MRD) from blood samples of patients with resected non-small cell lung carcinoma (NSCLC) is promising and opens up many opportunities for the optimisation of patient care in daily practice. Notably, this includes the potential for escalation or de-escalation of adjuvant therapies. Thus, the evaluation of MRD status can directly contribute to an increase in the overall survival of early stage NSCLC patients and/or limit therapeutic but also "financial" toxicity. Therefore, several clinical trials recently evaluated MRD in early stage NSCLC by integrating and retrospectively comparing the results of MRD assessments. In this context, there is an urgent need to close the gap between clinical research and the use of the evaluation of MRD in routine daily practice. Further action needs to be taken, particularly in evaluating the pertinence of the detection of MRD in prospective interventional clinical studies. This may be done in part by comparing different parameters, such as the techniques used, the different time points and the cutoffs of MRD assessments. This article investigates the assessment of MRD in non-small cell lung cancers, with a special focus on the issues associated with the various assays and the limitations of using circulating free DNA analyses for MRD assessment in early stage lung cancer. Recommendations and tips for the optimisation of MRD evaluation in non-small cell lung cancers are provided.
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Affiliation(s)
- Paul Hofman
- FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, Nice, France
| | - Marc G Denis
- Department of Biochemistry, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, Nantes Université, CHU Nantes, Nantes, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bu Q, Luo X, He L, Ma J, He S, Lei W, Zhou W, Deng H, Lin Y, Zhang L, Hong X. Septin9 DNA methylation as a promising biomarker for cervical cancer. J OBSTET GYNAECOL 2023; 43:2151356. [PMID: 36476308 DOI: 10.1080/01443615.2022.2151356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant Septin9 methylation in cervical cancer has been rarely studied. We aimed to identify its diagnostic value in cervical cancer using cervical scrapings, and its predictive potential in plasma for pelvic nodal metastasis of cervical cancer. The statuses of methylated Septin9 in fresh cervical lesions and cervical scrapings were first evaluated by using quantitative methylation-specific PCR. Subsequently, the relationship between Septin9 methylation in 113 plasma samples and pelvic nodal metastasis of cervical cancer was evaluated. Methylated Septin9 was detected in all cancerous tissues, but not in cervicitis. The degrees of Septin9 methylation increased with growing severity of cervical lesions in cervical scrapings. The sensitivity of methylated Septin9 was lower than that of cytology, while it yielded a high specificity and area under the curve in detecting high-grade squamous intraepithelial lesion or cervical cancer; and when Septin9 methylation combined with HPV16/18 genotyping, the sensitivity would increase from 70.42% to 82.39%. Plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%. In conclusion, we demonstrated methylated Septin9 to be an innovative diagnostic biomarker for cervical cancer and its non-invasive predictive potential in plasma for pelvic nodal metastasis of cervical cancer.Impact statementWhat is already known on this subject? The occurrence of cervical cancer is related to Septin9 methylation. In fresh specimens and cervical scrapings, we found the degrees of methylated Septin9 increased with growing severity of cervical lesions. Compared with HPV16/18 genotyping and cytological detection, Septin9 methylation had a better specificity and AUC in detecting ≥ HSIL. Furthermore, plasma-based Septin9 methylation also had a high specificity for pelvic lymphatic metastasis prediction.What the results of this study add? Methylation analysis of Septin9 indicated a similar sensitivity, specificity and AUC in detecting ≥ HSIL, relative to HPV16/18 genotyping. Compared with cytological method, Septin9 methylation also yielded a higher specificity and AUC in detecting ≥ HSIL. And we also found plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%; additionally an increasing sensitivity from 50% to nearly 80% was found when combined with SCCAg.What the implications are of these findings for clinical practice and/or further research? This study aimed to evaluate the relationship between Septin9 methylation and cervical cancer, and to explore the value of methylated Septin9 in the detection of cervical (pre)cancerous lesions. Moreover, we would explore plasma-based ctDNA biomarkers for pelvic lymphatic metastasis prediction of cervical cancer, to improve non-invasive predictive accuracy of pelvic nodal metastasis and reduce the complications caused by pelvic lymphadenectomy.
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Affiliation(s)
- Qiaowen Bu
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiping Luo
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lulu He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jian Ma
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shaoyi He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Weiping Zhou
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yu Lin
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaoshan Hong
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
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To YH, Gibbs P, Tie J, Loree J, Glyn T, Degeling K. Circulating Tumour DNA Guided Adjuvant Chemotherapy Decision Making in Stage II Colon Cancer-A Clinical Vignette Study. Cancers (Basel) 2023; 15:5227. [PMID: 37958401 PMCID: PMC10648421 DOI: 10.3390/cancers15215227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Circulating tumour DNA (ctDNA) is a promising biomarker that may better identify stage II colon cancer (CC) patients who will benefit from adjuvant chemotherapy (AC) compared to standard clinicopathological parameters. The DYNAMIC study demonstrated that ctDNA-informed treatment decreased AC utilisation without compromising recurrence free survival, but medical oncologists' willingness to utilise ctDNA results to inform AC decision is unknown. Medical oncologists from Australia, Canada and New Zealand were presented with clinical vignettes for stage II CC comprised of two variables with three levels each (age: ≤50, 52-69, ≥70 years; and clinicopathological risk of recurrence: low, intermediate, high) and were queried about ctDNA testing and treatment recommendations based on results. Sixty-four colorectal oncologists completed at least one vignette (all vignettes, n = 59). The majority of oncologist were Australian (70%; Canada: n = 13; New Zealand: n = 6) and had over 10 years of clinical experience (n = 41; 64%). The proportion of oncologists requesting ctDNA testing exceeded 80% for all vignettes, except for age ≥ 70 and low-risk disease (63%). Following a positive ctDNA result, the proportion of oncologists recommending AC (p < 0.01) and recommending oxaliplatin-based doublet (p < 0.01) increased in all vignettes. Following a negative result, the proportion recommending AC decreased in all intermediate and high-risk vignettes (p < 0.01).
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Affiliation(s)
- Yat Hang To
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3000, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Peter Gibbs
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3000, Australia
- Department of Medical Oncology, Western Health, St Albans, VIC 3091, Australia
- Faculty of Medicine & Health Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jeanne Tie
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3000, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Faculty of Medicine & Health Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jonathan Loree
- Division of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Tamara Glyn
- Department of Surgery, University of Otago, Christchurch 8011, New Zealand;
- Department of Surgery, Te Whatu Ora Health New Zealand Waitaha Canterbury, Christchurch 8140, New Zealand
| | - Koen Degeling
- Cancer Health Services Research, Centre for Cancer Research, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
- Cancer Health Services Research, Centre for Health Policy, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
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9
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Ang YLE, Zhao X, Reungwetwattana T, Cho BC, Liao BC, Yeung R, Loong HH, Kim DW, Yang JCH, Lim SM, Ahn MJ, Lee SH, Suwatanapongched T, Kongchauy K, Ou Q, Yu R, Tai BC, Goh BC, Mok TSK, Soo RA. A Phase II Study of Osimertinib in Patients with Advanced-Stage Non-Small Cell Lung Cancer following Prior Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor (EGFR TKI) Therapy with EGFR and T790M Mutations Detected in Plasma Circulating Tumour DNA (PLASMA Study). Cancers (Basel) 2023; 15:4999. [PMID: 37894366 PMCID: PMC10605750 DOI: 10.3390/cancers15204999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) T790M mutations drive resistance in 50% of patients with advanced non-small cell lung cancer (NSCLC) who progress on first/second generation (1G/2G) EGFR tyrosine kinase inhibitors (TKIs) and are sensitive to Osimertinib. Tissue sampling is the gold-standard modality of T790M testing, but it is invasive. We evaluated the efficacy of Osimertinib in patients with EGFR mutant NSCLC and T790M in circulating tumour DNA (ctDNA). PLASMA is a prospective, open-label, multicentre single-arm Phase II study. Patients with advanced NSCLC harbouring sensitizing EGFR and T790M mutations in plasma at progression from ≥one 1G/2G TKI were treated with 80 mg of Osimertinib daily until progression. The primary endpoint was the objective response rate (ORR); the secondary endpoints included progression-free survival (PFS), overall survival (OS), disease control rate (DCR) and toxicities. Plasma next-generation sequencing was performed to determine Osimertinib resistance mechanisms and assess serial ctDNA. A total of 110 patients from eight centres in five countries were enrolled from 2017 to 2019. The median follow-up duration was 2.64 (IQR 2.44-3.12) years. The ORR was 50.9% (95% CI 41.2-60.6) and the DCR was 84.5% (95% CI 76.4-90.7). Median PFS was 7.4 (95% CI 6.0-9.3) months; median OS was 1.63 (95% CI 1.35-2.16) years. Of all of the patients, 76% had treatment-related adverse events (TRAEs), most commonly paronychia (22.7%); 11% experienced ≥ Grade 3 TRAEs. The ctDNA baseline load and dynamics were prognostic. Osimertinib is active in NSCLC harbouring sensitizing EGFR and T790M mutations in ctDNA testing post 1G/2G TKIs.
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Affiliation(s)
- Yvonne L. E. Ang
- Department of Haematology-Oncology, National University Cancer Institute, Singapore 119074, Singapore
| | - Xiaotian Zhao
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing 210032, China
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Byoung-Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Bin-Chi Liao
- Department of Oncology, National Taiwan University Hospital, Taipei 100229, Taiwan
- National Taiwan University Cancer Center, Taipei 100229, Taiwan
| | - Rebecca Yeung
- Clinical Oncology Department, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong
| | - Herbert H. Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Central Ave, Hong Kong
| | - Dong-Wan Kim
- Seoul National University College of Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - James Chih-Hsin Yang
- Department of Oncology, National Taiwan University Hospital, Taipei 100229, Taiwan
- National Taiwan University Cancer Center, Taipei 100229, Taiwan
| | - Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Myung-Ju Ahn
- Division of Haematology-Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (M.-J.A.); (S.-H.L.)
| | - Se-Hoon Lee
- Division of Haematology-Oncology, Samsung Medical Center, Seoul 06351, Republic of Korea; (M.-J.A.); (S.-H.L.)
| | - Thitiporn Suwatanapongched
- Division of Diagnostic Radiology, Department of Diagnostic and Therapeutic Radiology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Kanchaporn Kongchauy
- Clinical Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Qiuxiang Ou
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing 210032, China
| | - Ruoying Yu
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing 210032, China
| | - Bee Choo Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, Singapore 119074, Singapore
| | - Tony S. K. Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Central Ave, Hong Kong
| | - Ross A. Soo
- Department of Haematology-Oncology, National University Cancer Institute, Singapore 119074, Singapore
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10
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Cohen R, Beasley A, McCoy M, Platell C, Meehan K, Gray E, Fuller K. Locally performed postoperative circulating tumour DNA testing performed during routine clinical care to predict recurrence of colorectal cancer. ANZ J Surg 2023; 93:2473-2480. [PMID: 36921099 DOI: 10.1111/ans.18385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND Identifying patients at high risk for colorectal cancer recurrence is essential for improving prognosis. In the postoperative period, circulating tumour DNA (ctDNA) has been demonstrated as a significant prognostic indicator of recurrence. These results have been obtained under the strict rigours of clinical trials, but not validated in a real-world setting using in-house testing. We report the outcomes of locally performed postoperative ctDNA testing conducted during routine clinical care and the association with the recurrence of colorectal cancer. METHODS We recruited 36 consecutive patients with newly diagnosed colorectal cancer between 2018 and 2020. Postoperative plasma samples were collected at the first outpatient review following resection. Tumour-informed ctDNA analysis was performed using droplet digital polymerase chain reaction or targeted next-generation sequencing. RESULTS At the time of surgery, there were 24 patients (66.7%) with localized cancer, nine (25%) with nodal spread, and three (8.3%) with metastatic disease. The median time from surgery to plasma sample donation was 22 days (IQR 20-28 days). At least one somatic mutation was identified in primary tumour tissue for 28 (77.8%) patients. Postoperative ctDNA was detected in five patients (13.9%). The median duration of follow-up was 32.0 months (IQR 27.2-38.1 months). Two patients (5.56%) developed metastatic recurrence. However, neither had detectable postoperative ctDNA. There were no instances of loco-regional recurrence. CONCLUSION Analysis of postoperative ctDNA testing can be performed locally, however this study did not reproduce the adverse association between detectable postoperative ctDNA and the development of colorectal cancer recurrence seen in clinical trials.
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Affiliation(s)
- Ryan Cohen
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Colorectal Research Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Aaron Beasley
- Centre for Precision Health, Edith Cowan University, Perth, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Melanie McCoy
- Colorectal Research Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Cameron Platell
- Colorectal Research Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Katie Meehan
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elin Gray
- Centre for Precision Health, Edith Cowan University, Perth, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Kathy Fuller
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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11
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Di Nardo L, Del Regno L, Di Stefani A, Mannino M, Fossati B, Catapano S, Quattrini L, Pellegrini C, Cortellini A, Parisi A, Capoluongo E, Autilio C, Fargnoli MC, Peris K. The dynamics of circulating tumour DNA (ctDNA) during treatment reflects tumour response in advanced melanoma patients. Exp Dermatol 2023; 32:1785-1793. [PMID: 37533342 DOI: 10.1111/exd.14901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
Despite the introduction of targeted (BRAFi/MEKi) and immune checkpoint inhibitors (ICIs) has significantly reduced the recurrence rate and improved the overall survival (OS) of patients with Stage III and IV melanoma, only a percentage will benefit of durable disease control. The aim of this study was to examine whether the levels of circulating tumour DNA (ctDNA) in plasma of advanced melanoma patients undergoing BRAFi/MEKi or ICIs vary according to the patients' survival outcomes (i.e. progression-free survival (PFS) and OS) and disease progression. Plasma samples of Stage III-IV melanoma patients were collected at baseline (treatment initiation) and thereafter every 3 months. Circulating BRAFV600E/K and NRASQ61R/K mutations were analysed through droplet digital PCR (ddPCR, Bio-Rad) in a total of 177 plasma samples from 48 melanoma patients (19 Stage III, 29 Stage IV). Baseline ctDNA concentration was significantly associated with OS (HR = 1.003, 95% CI = 1.000-1.006, p = 0.043) and PFS (HR = 1.004, 95% CI = 1.000-1.007, p = 0.029) independent of clinical-prognostic confounders. For each unit increase in the ∆ctDNA (concentration difference between the last follow-up and baseline) there was a 24% increased risk of disease progression, irrespective of treatment type and stage at diagnosis (OR = 1.24, 95% CI = 1.03-1.49, p = 0.020, AUC = 0.93). Patients with reduction of ctDNA level from baseline to the last follow-up had longer OS (HR = 0.14; 95% CI = 0.05-0.44, p = 0.001) and PFS (HR = 0.08; 95% CI = 0.03-0.27, p < 0.0001) compared to patients with increased ctDNA, including adjustment for confounding factors. Our findings suggest that variation of ctDNA over time during melanoma treatment reflects the clinical outcome and tumour response to therapy and might be helpful in clinical monitoring.
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Affiliation(s)
- Lucia Di Nardo
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Laura Del Regno
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Alessandro Di Stefani
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Maria Mannino
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Barbara Fossati
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Silvia Catapano
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Laura Quattrini
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Alessio Cortellini
- Medical Oncology Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Alessandro Parisi
- Department of Oncology, Università Politecnica delle Marche, Azienda Ospedaliero-Universitaria Ospedali Riuniti di Ancona, Ancona, Italy
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Naples, Italy
- CEINGE, Advanced Biotechnology, Naples, Italy
- Department of Clinical Pathology and Genomics, Ospedale Cannizzaro, Catania, Italy
| | - Chiara Autilio
- Department of Biochemistry and Molecular Biology and Research Institute Hospital, Complutense University, Madrid, Spain
| | - Maria Concetta Fargnoli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Ketty Peris
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
- UOC di Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A, Gemelli - IRCCS, Rome, Italy
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12
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Chen JW, Jacot W, Cortés J, Krop IE, Dent S, Harbeck N, De Laurentiis M, Diéras V, Im Y, Stout TJ, Schimmoller F, Savage HM, Hutchinson KE, Wilson TR. ER+, HER2- advanced breast cancer treated with taselisib and fulvestrant: genomic landscape and associated clinical outcomes. Mol Oncol 2023; 17:2000-2016. [PMID: 36892268 PMCID: PMC10552898 DOI: 10.1002/1878-0261.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 03/10/2023] Open
Abstract
Taselisib is a potent β-sparing phosphatidylinositol 3-kinase (PI3K) inhibitor that, with endocrine therapy, improves outcomes in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA)-mutated (PIK3CAmut) advanced breast cancer. To understand alterations associated with response to PI3K inhibition, we analysed circulating tumour DNA (ctDNA) from participants enrolled in the SANDPIPER trial. Participants were designated as either PIK3CAmut or PIK3CA no mutation was detected (NMD) per baseline ctDNA. The top mutated genes and tumour fraction estimates identified were analysed for their association with outcomes. In participants with PIK3CAmut ctDNA treated with taselisib + fulvestrant, tumour protein p53 (TP53; encoding p53) and fibroblast growth factor receptor 1 (FGFR1) alterations were associated with shorter progression-free survival (PFS) compared to participants with NMD in these genes. Conversely, participants with PIK3CAmut ctDNA harbouring a neurofibromin 1 (NF1) alteration or high baseline tumour fraction estimate experienced improved PFS upon treatment with taselisib + fulvestrant compared to placebo + fulvestrant. Broadly, alterations in oestrogen receptor (ER), PI3K and p53 pathway genes were associated with resistance to taselisib + fulvestrant in participants with PIK3CAmut ctDNA. Altogether, we demonstrated the impact of genomic (co-)alterations on outcomes with one of the largest clinico-genomic datasets of ER+, HER2-, PIK3CAmut breast cancer patients treated with a PI3K inhibitor.
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Affiliation(s)
- Jessica W. Chen
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
| | - William Jacot
- Institut du Cancer de Montpellier (ICM) Val d'AurelleMontpellier University, INSERM U1194France
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea OncologyQuironsalud GroupMadridSpain
- International Breast Cancer Center (IBCC), Pangaea OncologyQuironsalud GroupBarcelonaSpain
- Faculty of Biomedical and Health Sciences, Department of MedicineUniversidad Europea de MadridMadridSpain
| | | | - Susan Dent
- Duke Cancer InstituteDuke UniversityDurhamNCUSA
| | - Nadia Harbeck
- Breast Center, Department Gynecology and Obstetrics and Comprehensive Cancer Center (CCC) MunichLudwig‐Maximilians‐University (LMU) HospitalMunichGermany
| | | | | | - Young‐Hyuck Im
- Division of Hematology‐Oncology, Department of Medicine, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Thomas J. Stout
- Product Development OncologyGenentech, Inc.South San FranciscoCAUSA
| | | | - Heidi M. Savage
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
| | | | - Timothy R. Wilson
- Oncology Biomarker DevelopmentGenentech, Inc.South San FranciscoCAUSA
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13
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Zhu JW, Wong F, Szymiczek A, Ene GEV, Zhang S, May T, Narod SA, Kotsopoulos J, Akbari MR. Evaluating the Utility of ctDNA in Detecting Residual Cancer and Predicting Recurrence in Patients with Serous Ovarian Cancer. Int J Mol Sci 2023; 24:14388. [PMID: 37762691 PMCID: PMC10532395 DOI: 10.3390/ijms241814388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Ovarian cancer has a high case fatality rate, but patients who have no visible residual disease after surgery have a relatively good prognosis. The presence of any cancer cells left in the peritoneal cavity after treatment may precipitate a cancer recurrence. In many cases, these cells are occult and are not visible to the surgeon. Analysis of circulating tumour DNA in the blood (ctDNA) may offer a sensitive method to predict the presence of occult (non-visible) residual disease after surgery and may help predict disease recurrence. We assessed 48 women diagnosed with serous ovarian cancer (47 high-grade and 1 low-grade) for visible residual disease and for ctDNA. Plasma, formalin-fixed paraffin-embedded (FFPE) tumour tissue and white blood cells were used to extract circulating free DNA (cfDNA), tumour DNA and germline DNA, respectively. We sequenced DNA samples for 59 breast and ovarian cancer driver genes. The plasma sample was collected after surgery and before initiating chemotherapy. We compared survival in women with no residual disease, with and without a positive plasma ctDNA test. We found tumour-specific variants (TSVs) in cancer cells from 47 patients, and these variants were sought in ctDNA in their post-surgery plasma. Fifteen (31.9%) of the 47 patients had visible residual disease; of these, all 15 had detectable ctDNA. Thirty-one patients (65.9%) had no visible residual disease; of these, 24 (77.4%) patients had detectable ctDNA. Of the patients with no visible residual disease, those patients with detectable ctDNA had higher mortality (20 of 27 died) than those without detectable ctDNA (3 of 7 died) (HR 2.32; 95% CI: 0.67-8.05), although this difference was not statistically significant (p = 0.18). ctDNA in post-surgical serum samples may predict the presence of microscopic residual disease and may be a predictor of recurrence among women with ovarian cancer. Larger studies are necessary to validate these findings.
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Affiliation(s)
- Jie Wei Zhu
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8P 1H6, Canada
| | - Fabian Wong
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Agata Szymiczek
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
| | - Gabrielle E. V. Ene
- Division of Gynecologic Oncology, Department of Surgical Oncology, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Shiyu Zhang
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
| | - Taymaa May
- Division of Gynecologic Oncology, Department of Surgical Oncology, Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2M9, Canada
- Division of Gynecologic Oncology, Department of Obstetric and Gynecology, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Steven A. Narod
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Joanne Kotsopoulos
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Mohammad R. Akbari
- Women’s College Research Institute, Women’s College Hospital, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
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14
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Petit J, Carroll G, Williams H, Pockney P, Scott RJ. Evaluation of a Multi-Gene Methylation Blood-Test for the Detection of Colorectal Cancer. Med Sci (Basel) 2023; 11:60. [PMID: 37755164 PMCID: PMC10534804 DOI: 10.3390/medsci11030060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
Circulating tumour DNA biomarkers are an expanding field in oncology research that offer great potential but are currently often limited in value by overall cost. The aim of this study was to evaluate the efficacy of a novel multi-gene methylation blood test for the identification of colorectal cancer and throughout the spectrum of colorectal disease. Participants were recruited either prior to resection for known CRC or prior to screening colonoscopy after a positive faecal immunochemical test. Blood was collected from participants prior to their procedure being performed. The plasma was separated, and multiplex MethylLight droplet digital PCR was used to analyse for the presence of four methylated genes: SDC2, NPY, IKZF1 and SEPT9. A total of 537 participants underwent analysis. The SDC2/NPY genes showed a sensitivity of 33-54% and a specificity of 72-96%, whilst the IKZF1/SEPT9 genes showed a sensitivity of 19-42% and a specificity of 88-96%. Combining the two tests did not significantly increase the test accuracy. The sensitivity for advanced adenoma was 2-15%. There was a significant difference in the frequency of detectable methylation between the participants with CRC and those without CRC. However, neither the sensitivity nor the specificity was superior to current diagnostic screening tests.
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Affiliation(s)
- Joel Petit
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Georgia Carroll
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Henry Williams
- Division of Surgery, John Hunter Hospital, Newcastle, NSW 2305, Australia
| | - Peter Pockney
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
| | - Rodney J. Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW 2305, Australia
- Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2305, Australia
- Pathology North, Newcastle, NSW 2305, Australia
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15
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Edland KH, Tjensvoll K, Oltedal S, Dalen I, Lapin M, Garresori H, Glenjen N, Gilje B, Nordgård O. Monitoring of circulating tumour DNA in advanced pancreatic ductal adenocarcinoma predicts clinical outcome and reveals disease progression earlier than radiological imaging. Mol Oncol 2023; 17:1857-1870. [PMID: 37341038 PMCID: PMC10483602 DOI: 10.1002/1878-0261.13472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 06/19/2023] [Indexed: 06/22/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a need for better tools to guide treatment selection and follow-up. The aim of this prospective study was to investigate the prognostic value and treatment monitoring potential of longitudinal circulating tumour DNA (ctDNA) measurements in patients with advanced PDAC undergoing palliative chemotherapy. Using KRAS peptide nucleic acid clamp-PCR, we measured ctDNA levels in plasma samples obtained at baseline and every 4 weeks during chemotherapy from 81 patients with locally advanced and metastatic PDAC. Cox proportional hazard regression showed that ctDNA detection at baseline was an independent predictor of progression-free and overall survival. Joint modelling demonstrated that the dynamic ctDNA level was a strong predictor of time to first disease progression. Longitudinal ctDNA measurements during chemotherapy successfully revealed disease progression in 20 (67%) of 30 patients with ctDNA detected at baseline, with a median lead time of 23 days (P = 0.01) over radiological imaging. Here, we confirmed the clinical relevance of ctDNA in advanced PDAC with regard to both the prediction of clinical outcome and disease monitoring during treatment.
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Affiliation(s)
| | - Kjersti Tjensvoll
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Satu Oltedal
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Ingvild Dalen
- Section of Biostatistics, Department of ResearchStavanger University HospitalNorway
| | - Morten Lapin
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Herish Garresori
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Nils Glenjen
- Department of OncologyHaukeland University HospitalBergenNorway
| | - Bjørnar Gilje
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Oddmund Nordgård
- Department of Hematology and OncologyStavanger University HospitalNorway
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and TechnologyUniversity of StavangerNorway
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16
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Sisodiya S, Kasherwal V, Khan A, Roy B, Goel A, Kumar S, Arif N, Tanwar P, Hussain S. Liquid Biopsies: Emerging role and clinical applications in solid tumours. Transl Oncol 2023; 35:101716. [PMID: 37327582 PMCID: PMC10285278 DOI: 10.1016/j.tranon.2023.101716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023] Open
Abstract
Late detection and lack of precision diagnostics are the major challenges in cancer prevention and management. Biomarker discovery in specific cancers, especially at the pre-invasive stage, is vital for early diagnosis, positive treatment response, and good disease prognosis. Traditional diagnostic measures require invasive procedures such as tissue excision using a needle, an endoscope, and/or surgical resection which can be unsafe, expensive, and painful. Additionally, the presence of comorbid conditions in individuals might render them ineligible for undertaking a tissue biopsy, and in some cases, it is difficult to access tumours depending on the site of occurrence. In this context, liquid biopsies are being explored for their clinical significance in solid malignancies management. These non-invasive or minimally invasive methods are being developed primarily for identification of biomarkers for early diagnosis and targeted therapeutics. In this review, we have summarised the use and importance of liquid biopsy as significant tool in diagnosis, prognosis prediction, and therapeutic development. We have also discussed the challenges that are encountered and future perspective.
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Affiliation(s)
- Sandeep Sisodiya
- Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India; Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University) (SIU), Pune, India
| | - Vishakha Kasherwal
- Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India; Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, India
| | - Asiya Khan
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India; Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Bishnudeo Roy
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University) (SIU), Pune, India
| | - Anjana Goel
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Sandeep Kumar
- Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Nazneen Arif
- Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Pranay Tanwar
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Showket Hussain
- Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India.
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17
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Kojima Y, Noguchi E, Yoshino T, Yagishita S, Yazaki S, Okuma HS, Nishikawa T, Tanioka M, Sudo K, Shimoi T, Kazama A, Terasaki H, Asano S, Fujiwara Y, Hamada A, Tamura K, Yonemori K. Development of a Detection System for ESR1 Mutations in Circulating Tumour DNA Using PNA-LNA-Mediated PCR Clamping. Diagnostics (Basel) 2023; 13:2040. [PMID: 37370935 DOI: 10.3390/diagnostics13122040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Although circulating tumour DNA (ctDNA)-based next-generation sequencing (NGS) is a less invasive method for assessing ESR1 mutations that are essential mechanisms of endocrine therapy resistance in patients with oestrogen receptor-positive breast cancer, adequate amounts of DNA are required to assess polyclonal ESR1 mutations. By combining a peptide nucleic acid and locked nucleic acid polymerase chain reaction (PNA-LNA PCR) clamping assay, we have developed a novel detection system to screen for polyclonal ESR1 mutations in ctDNA. A validation assay was prospectively performed on clinical samples and compared with the NGS results. The PNA-LNA PCR clamp assay was validated using six and four blood samples in which ESR1 mutations were detected by NGS and no mutations were detected, respectively. The PNA-LNA assay results were comparable with those of NGS. We prospectively assessed the concordance between the PNA-LNA PCR clamp method and NGS. Using the PNA-LNA PCR clamp method, ESR1 mutations were detected in 5 out of 18 samples, including those in which mutations were not detected by NGS due to small amounts of ctDNA. The PNA-LNA PCR clamping method is a highly sensitive and minimally invasive assay for polyclonal ESR1 mutation detection in the ctDNA of patients with breast cancer.
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Affiliation(s)
- Yuki Kojima
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Emi Noguchi
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Tomomi Yoshino
- Department of Pharmacology and Therapeutics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Shigehiro Yagishita
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Shu Yazaki
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Hitomi S Okuma
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Tadaaki Nishikawa
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Maki Tanioka
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Kazuki Sudo
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Tatsunori Shimoi
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Ayaka Kazama
- Molecular Genetic Research Department, LSI Medience Corporation, Shimura 3-30-1, Itabashi-ku, Tokyo 174-8555, Japan
| | - Hiroshi Terasaki
- Molecular Genetic Research Department, LSI Medience Corporation, Shimura 3-30-1, Itabashi-ku, Tokyo 174-8555, Japan
| | - Sachiro Asano
- Life Technologies Japan Ltd., Thermo Fisher Scientific, Shibaura 4-2-8, Minato-ku, Tokyo 108-0023, Japan
| | - Yasuhiro Fujiwara
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
- Department of Pharmacology and Therapeutics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Kenji Tamura
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
| | - Kan Yonemori
- Department of Medical Oncology, National Cancer Center Hospital, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan
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18
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Frontiers Production Office. Erratum: Application of circulating tumour DNA in terms of prognosis prediction in chinese follicular lymphoma patients. Front Genet 2023; 14:1228830. [PMID: 37333497 PMCID: PMC10272842 DOI: 10.3389/fgene.2023.1228830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1066808.].
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19
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Wei C, Wang W, Zhang Y, Zhao D, Zhang W, Zhou D. Mutation profiling, tumour burden assessment, outcome prediction and disease monitoring by circulating tumour DNA in peripheral T-cell lymphoma. Br J Haematol 2023. [PMID: 37132364 DOI: 10.1111/bjh.18824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
In this prospective study, we aimed to evaluate the utility of circulating tumour DNA (ctDNA) in peripheral T-cell lymphomas (PTCLs). Plasma cell-free DNA (cfDNA) was obtained, and the mutational profile was assessed in 47 patients with newly diagnosed mature T- and NK-cell lymphoma. To validate the mutations detected in cfDNA, paired tumour tissue samples were available for 36 patients. Targeted next-generation sequencing was performed. A total of 279 somatic mutations involving 149 genes were identified in the 47 cfDNA samples. The overall sensitivity of plasma cfDNA in discovering biopsy-confirmed mutations was 73.9% with a specificity of 99.6%. When we considered only mutations with variant allele frequency >5% in the tumour biopsy, the sensitivity increased to 81.9%. Pretreatment ctDNA concentration and the number of mutations were highly correlated with tumour burden indicators including lactate dehydrogenase, Ann Arbor stage and International Prognostic Index score. Patients with high ctDNA level (>1.9 log ng/mL) had significantly lower overall response rates, inferior 1-year progression-free survival and overall survival rates than those with low level. Longitudinal analysis of ctDNA showed a strong agreement between ctDNA dynamics and the radiographic response. In conclusion, our study demonstrates that ctDNA may serve as a promising tool for mutational profiling, tumour burden assessment, outcome prediction and disease monitoring in PTCLs.
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Affiliation(s)
- Chong Wei
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Zhang
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Danqing Zhao
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhang
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daobin Zhou
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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20
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Zaman FY, Subramaniam A, Afroz A, Samoon Z, Gough D, Arulananda S, Alamgeer M. Circulating Tumour DNA (ctDNA) as a Predictor of Clinical Outcome in Non-Small Cell Lung Cancer Undergoing Targeted Therapies: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:cancers15092425. [PMID: 37173891 PMCID: PMC10177293 DOI: 10.3390/cancers15092425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Liquid biopsy (LB) analysis using (ctDNA)/cell-free DNA (cfDNA) is an emerging alternative to tissue profiling in (NSCLC). LB is used to guide treatment decisions, detect resistance mechanisms, and predicts responses, and, therefore, outcomes. This systematic review and meta-analysis evaluated the impact of LB quantification on clinical outcomes in molecularly altered advanced NSCLC undergoing targeted therapies. METHODS We searched Embase, MEDLINE, PubMed, and Cochrane Database, between 1 January 2020 and 31 August 2022. The primary outcome was progression-free survival (PFS). Secondary outcomes included overall survival (OS), objective response rate (ORR), sensitivity, and specificity. Age stratification was performed based on the mean age of the individual study population. The quality of studies was assessed using the Newcastle-Ottawa Scale (NOS). RESULTS A total of 27 studies (3419 patients) were included in the analysis. Association of baseline ctDNA with PFS was reported in 11 studies (1359 patients), while that of dynamic changes with PFS was reported in 16 studies (1659 patients). Baseline ctDNA-negative patients had a trend towards improved PFS (pooled hazard ratio [pHR] = 1.35; 95%CI: 0.83-1.87; p < 0.001; I2 = 96%) than ctDNA-positive patients. Early reduction/clearance of ctDNA levels after treatment was related to improved PFS (pHR = 2.71; 95%CI: 1.85-3.65; I2 = 89.4%) compared to those with no reduction/persistence in ctDNA levels. The sensitivity analysis based on study quality (NOS) demonstrated improved PFS only for good [pHR = 1.95; 95%CI: 1.52-2.38] and fair [pHR = 1.99; 95%CI: 1.09-2.89] quality studies, but not for poor quality studies. There was, however, a high level of heterogeneity (I2 = 89.4%) along with significant publication bias in our analysis. CONCLUSIONS This large systematic review, despite heterogeneity, found that baseline negative ctDNA levels and early reduction in ctDNA following treatment could be strong prognostic markers for PFS and OS in patients undergoing targeted therapies for advanced NSCLC. Future randomised clinical trials should incorporate serial ctDNA monitoring to further establish the clinical utility in advanced NSCLC management.
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Affiliation(s)
- Farzana Y Zaman
- Department of Medical Oncology, Monash Health, Clayton 3168, Australia
| | - Ashwin Subramaniam
- School of Public Health and Preventive Medicine, Monash University, Clayton 3168, Australia
- Department of Intensive Care, Peninsula Health, Frankston 3199, Australia
- Peninsula Clinical School, Monash University, Frankston 3199, Australia
| | - Afsana Afroz
- School of Public Health and Preventive Medicine, Monash University, Clayton 3168, Australia
| | - Zarka Samoon
- Department of Medical Oncology, Monash Health, Clayton 3168, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton 3168, Australia
| | - Surein Arulananda
- Department of Medical Oncology, Monash Health, Clayton 3168, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton 3168, Australia
- School of Clinical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton 3168, Australia
| | - Muhammad Alamgeer
- Department of Medical Oncology, Monash Health, Clayton 3168, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton 3168, Australia
- School of Clinical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton 3168, Australia
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21
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Le Goff E, Blanc-Durand P, Roulin L, Lafont C, Loyaux R, MBoumbae DL, Benmaad I, Claudel A, Poullot E, Robe C, Gricourt G, Aissat A, Copie-Bergman C, Lemonnier F, Gaulard P, Itti E, Haioun C, Delfau-Larue MH. Baseline circulating tumour DNA and total metabolic tumour volume as early outcome predictors in aggressive large B-cell lymphoma. A real-world 112-patient cohort. Br J Haematol 2023. [PMID: 37038217 DOI: 10.1111/bjh.18809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/12/2023]
Abstract
Approximately 20%-50% of patients with large B-cell lymphoma (LBCL) experience poor outcomes. We aimed to evaluate the combined prognostic value of circulating tumour DNA (ctDNA) and total metabolic tumour volume (TMTV) in LBCL. This observational single-centre study included 112 newly diagnosed LBCL patients, receiving R-CHOP/R-CHOP-like chemotherapies. CtDNA load was calculated following next-generation sequencing of cell-free DNA (cfDNA) using a targeted 40-gene lymphopanel. TMTV was measured using a fully automated artificial intelligence-based method for lymphoma lesion segmentation. CtDNA was detected in cfDNA samples from 95 patients with a median concentration of 3.15 log haploid genome equivalents per mL. TMTV measurements were available for 102 patients. The median TMTV was 501 mL. High ctDNA load (>3.57 log hGE/mL) or high TMTV (>200 mL) were associated with shorter 1-year PFS (44% vs. 83%, p < 0.001 and 64% vs. 97%, p = 0.002, respectively). When combined, three prognostic groups were identified. The shortest PFS was observed when both TMTV and ctDNA load were high (p < 0.001). Even with a short follow up, combining ctDNA load with TMTV improved the risk stratification of patients with aggressive LBCL. In the near future, very high-risk patients could benefit from CAR T-cell therapy or bispecific antibodies as first-line treatments.
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Affiliation(s)
- Enora Le Goff
- Lymphoid Malignancies Unit, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Paul Blanc-Durand
- Nuclear Medicine Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
| | - Louise Roulin
- Lymphoid Malignancies Unit, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Charlotte Lafont
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
- Public Health Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Romain Loyaux
- Hematobiology and Immunobiology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Diana-Laure MBoumbae
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
- Hematobiology and Immunobiology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Ichrafe Benmaad
- Hematobiology and Immunobiology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Alexis Claudel
- Hematobiology and Immunobiology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Elsa Poullot
- Pathology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Cyrielle Robe
- Pathology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Guillaume Gricourt
- Bioinformatics Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Abdelrazak Aissat
- Bioinformatics Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Christiane Copie-Bergman
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
- Pathology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - François Lemonnier
- Lymphoid Malignancies Unit, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
| | - Philippe Gaulard
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
- Pathology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
| | - Emmanuel Itti
- Nuclear Medicine Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
| | - Marie-Helene Delfau-Larue
- Paris-Est Créteil University, INSERM, IMRB, F-94010, Créteil, France
- Hematobiology and Immunobiology Department, Assistance Publique des Hôpitaux de Paris, HU Henri Mondor, Créteil, France
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22
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Strati A, Markou A, Kyriakopoulou E, Lianidou E. Detection and Molecular Characterization of Circulating Tumour Cells: Challenges for the Clinical Setting. Cancers (Basel) 2023; 15:cancers15072185. [PMID: 37046848 PMCID: PMC10092977 DOI: 10.3390/cancers15072185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Over the last decade, liquid biopsy has gained much attention as a powerful tool in personalized medicine since it enables monitoring cancer evolution and follow-up of cancer patients in real time. Through minimally invasive procedures, liquid biopsy provides important information through the analysis of circulating tumour cells (CTCs) and circulating tumour-derived material, such as circulating tumour DNA (ctDNA), circulating miRNAs (cfmiRNAs) and extracellular vehicles (EVs). CTC analysis has already had an important impact on the prognosis, detection of minimal residual disease (MRD), treatment selection and monitoring of cancer patients. Numerous clinical trials nowadays include a liquid biopsy arm. CTC analysis is now an exponentially expanding field in almost all types of solid cancers. Functional studies, mainly based on CTC-derived cell-lines and CTC-derived explants (CDx), provide important insights into the metastatic process. The purpose of this review is to summarize the latest findings on the clinical significance of CTCs for the management of cancer patients, covering the last four years. This review focuses on providing a comprehensive overview of CTC analysis in breast, prostate and non-small-cell lung cancer. The unique potential of CTC single-cell analysis for understanding metastasis biology, and the importance of quality control and standardization of methodologies used in this field, is also discussed.
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Affiliation(s)
- Areti Strati
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Athina Markou
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | | | - Evi Lianidou
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
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23
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Horndalsveen H, Alver TN, Dalsgaard AM, Rogg LV, Helbekkmo N, Grønberg BH, Halvorsen TO, Ramberg C, Haakensen VD, Öjlert ÅK, Bjaanaes MM, Helland Å. Atezolizumab and stereotactic body radiotherapy in patients with advanced non-small cell lung cancer: safety, clinical activity and ctDNA responses-the ComIT-1 trial. Mol Oncol 2023; 17:487-498. [PMID: 36330681 PMCID: PMC9980306 DOI: 10.1002/1878-0261.13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/02/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The introduction of immune checkpoint inhibitors has transformed the treatment landscape of metastatic non-small cell lung cancer. However, challenges remain to increase the fraction of patients achieving durable clinical responses to these drugs and to help monitor the treatment effect. In this phase II trial, we investigated the toxicity, systemic responses and circulating tumour DNA responses in patients (n = 21) with advanced non-small-cell lung cancer treated with atezolizumab and stereotactic body radiotherapy in the second or later line. We found the combined treatment to be safe with grade 3 toxicity reported in three patients. As the best overall response, four patients had a partial response, eight had stable disease and five had progressive disease. Median overall survival time was still not reached after a median follow-up of 26.5 months and 10/15 patients with programmed death-ligand 1 negative tumours were alive >18 months after the start of the study treatment. ctDNA was detectable at baseline in 11 patients. A rapid decline in ctDNA to <30% of baseline levels was seen in three patients, two of which were radiographic responders and one was considered clinically benefiting from therapy for almost 1 year.
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Affiliation(s)
- Henrik Horndalsveen
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Tine Norman Alver
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway.,Department of Clinical Medicine, University of Oslo, Norway
| | - Astrid Marie Dalsgaard
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | | | - Nina Helbekkmo
- Department of Pulmonology, University Hospital of North Norway, Tromsø, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Norway
| | | | - Vilde Drageset Haakensen
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Åsa Kristina Öjlert
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | | | - Åslaug Helland
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway.,Department of Clinical Medicine, University of Oslo, Norway
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24
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Eyck BM, Jansen MP, Noordman BJ, Atmodimedjo PN, van der Wilk BJ, Martens JW, Helmijr JA, Beaufort CM, Mostert B, Doukas M, Wijnhoven BP, Lagarde SM, van Lanschot JJB, Dinjens WN. Detection of circulating tumour DNA after neoadjuvant chemoradiotherapy in patients with locally advanced oesophageal cancer. J Pathol 2023; 259:35-45. [PMID: 36196486 PMCID: PMC10092085 DOI: 10.1002/path.6016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/05/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Active surveillance instead of standard surgery after neoadjuvant chemoradiotherapy (nCRT) has been proposed for patients with oesophageal cancer. Circulating tumour DNA (ctDNA) may be used to facilitate selection of patients for surgery. We show that detection of ctDNA after nCRT seems highly suggestive of major residual disease. Tumour biopsies and blood samples were taken before, and 6 and 12 weeks after, nCRT. Biopsies were analysed with regular targeted next-generation sequencing (NGS). Circulating cell-free DNA (cfDNA) was analysed using targeted NGS with unique molecular identifiers and digital polymerase chain reaction. cfDNA mutations matching pre-treatment biopsy mutations confirmed the presence of ctDNA. In total, 31 patients were included, of whom 24 had a biopsy mutation that was potentially detectable in cfDNA (77%). Pre-treatment ctDNA was detected in nine of 24 patients (38%), four of whom had incurable disease progression before surgery. Pre-treatment ctDNA detection had a sensitivity of 47% (95% CI 24-71) (8/17), specificity of 85% (95% CI 42-99) (6/7), positive predictive value (PPV) of 89% (95% CI 51-99) (8/9), and negative predictive value (NPV) of 40% (95% CI 17-67) (6/15) for detecting major residual disease (>10% residue in the resection specimen or progression before surgery). After nCRT, ctDNA was detected in three patients, two of whom had disease progression. Post-nCRT ctDNA detection had a sensitivity of 21% (95% CI 6-51) (3/14), specificity of 100% (95% CI 56-100) (7/7), PPV of 100% (95% CI 31-100) (3/3), and NPV of 39% (95% CI 18-64) (7/18) for detecting major residual disease. The addition of ctDNA to the current set of diagnostics did not lead to more patients being clinically identified with residual disease. These results indicate that pre-treatment and post-nCRT ctDNA detection may be useful in identifying patients at high risk of disease progression. The addition of ctDNA analysis to the current set of diagnostic modalities may not improve detection of residual disease after nCRT. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ben M Eyck
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Maurice Phm Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bo Jan Noordman
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Berend J van der Wilk
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - John Wm Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bas Pl Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Sjoerd M Lagarde
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Winand Nm Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
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25
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Zhao M, Li Q, Yang J, Zhang M, Liu X, Zhang H, Huang Y, Li J, Bao J, Wang J, Du J, Guan T, Su L. Application of circulating tumour DNA in terms of prognosis prediction in Chinese follicular lymphoma patients. Front Genet 2023; 14:1066808. [PMID: 37152994 PMCID: PMC10157236 DOI: 10.3389/fgene.2023.1066808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Follicular lymphoma (FL), an indolent non-Hodgkin lymphoma (NHL), is generally incurable. Favourable prognosis and durable remission are crucial for FL patients. The genetic mutation spectrum provides novel biomarkers for determining the prognosis of FL patients, but its detection is easily affected by the collection of tumour tissue biopsies. In this study, we aimed to describe the mutational landscape of FL using circulating tumour DNA (ctDNA) samples and to explore the relationship between mutations and prognostic indicators of clinical outcome in patients with newly diagnosed follicular lymphoma and the prognostic value of such mutations. Methods: A total of 28 patients with newly diagnosed FL were included in this study. A targeted NGS-based 59-gene panel was used to assess the ctDNA mutation profiles. Differences in clinical factors between patients carrying mutations and those without mutations were analysed. We also explored the relationship between gene mutation status, mean VAFs (variant allele frequencies) and clinical factors. The Kaplan‒Meier method was applied to analyse the overall survival (OS) and progression-free survival (PFS) of patients carrying mutations and those without mutations. Results: ctDNA mutations were detectable in 21 (75%) patients. The most commonly mutated genes were CREBBP (54%, 15/28), KMT2D (50%, 14/28), STAT6 (29%, 8/28), CARD11 (18%, 5/28), PCLO (14%, 4/28), EP300 (14%, 4/28), BCL2 (11%, 3/28), and TNFAIP3 (11%, 3/28), with a mutation frequency of >10%. Patients with detectable ctDNA mutation tended to present with advanced Ann Arbor stage (III-IV) (p = 0.009), high FLIPI risk (3-5) (p = 0.023) and severe lymph node involvement (No. of involved areas ≥5) (p = 0.02). In addition, we found that the mean VAF was significantly higher in patients with advanced Ann Arbor stage, high-risk FLIPI, elevated lactate dehydrogenase (LDH: 0-248U/L), advanced pathology grade, bone marrow involvement (BMI) and lymph node involvement. Additionally, KMT2D, EP300, and STAT6 mutations were associated with inferior PFS (p < 0.05). Conclusion: We described the ctDNA mutation landscapes in Chinese patients with newly diagnosed FL and found that ctDNA VAF means reflect tumour burden. Moreover, PFS was shorter in patients with KMT2D, EP300 and STAT6 mutations.
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Affiliation(s)
- Mengjing Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, China
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Qingjuan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, China
| | - Jing Yang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Min Zhang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Xiaolan Liu
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Hongwei Zhang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Yunpeng Huang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jing Li
- Department of Pathology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jiangping Bao
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jingfang Wang
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Guan
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Tao Guan, ; Liping Su,
| | - Liping Su
- Department of Hematology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Tao Guan, ; Liping Su,
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Mi J, Han X, Wang R, Ma R, Zhao D. Circulation tumour DNA in predicting recurrence and prognosis in operable colorectal cancer patients: A meta-analysis. Eur J Clin Invest 2022; 52:e13842. [PMID: 35856399 DOI: 10.1111/eci.13842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Selecting the appropriate patient for further treatment after surgery and adjuvant chemotherapy (ACT) for colorectal cancer (CRC) can improve the patient's prognosis. Circulating tumour DNA (ctDNA) has the potential to predict recurrence and prognosis after CRC surgery and ACT, but the results are still inconclusive. OBJECTIVES As the completed studies have small sample sizes and different experimental methods, a meta-analysis was conducted to assess the ctDNA on recurrence and prognosis after CRC surgery and ACT. METHODS PubMed, Embase, the Web of Science and the Cochrane Library were searched for potentially eligible studies published up to 6 March 2022. Pooled relative risk (RR) and pooled hazard ratio (HR) were calculated to evaluate recurrence and the prognosis of recurrence-free survival (RFS) following CRC surgery and ACT. RESULTS Fourteen studies published between 2014 and 2022 included 2393 patients, and 7189 serum samples were eventually included in the meta-analysis. The pooled revealed that ctDNA-positive patients were at high risk of recurrence after CRC surgery (RR = 4.43, 95% CI: 3.58-5.48, p < .05) and had a poorer prognosis for RFS (HR = 7.26, 95% CI: 5.48-9.62, p < .05). The pooled revealed that ctDNA-positive patients were at high risk of recurrence after ACT (RR = 5.77 95% CI: 4.33-7.69, p < .05) and had a poorer prognosis for RFS (HR = 13.96, 95% CI: 8.71-22.4, p < .05). CONCLUSION ctDNA-positive patients were at a high risk of recurrence after CRC surgery and ACT and had a poorer prognosis. Hence, ctDNA-positive patients required close follow-up and further treatments.
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Affiliation(s)
- Junjie Mi
- Digestive Endoscopy Center, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Xiaofang Han
- Reproductive Medicine, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Rong Wang
- Digestive Endoscopy Center, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Ruijun Ma
- Digestive Endoscopy Center, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Danyu Zhao
- Digestive Endoscopy Center, Shanxi Provincial People's Hospital, Taiyuan, China
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Saman H, Raza A, Patil K, Uddin S, Crnogorac-Jurcevic T. Non-Invasive Biomarkers for Early Lung Cancer Detection. Cancers (Basel) 2022; 14. [PMID: 36497263 DOI: 10.3390/cancers14235782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Worldwide, lung cancer (LC) is the most common cause of cancer death, and any delay in the detection of new and relapsed disease serves as a major factor for a significant proportion of LC morbidity and mortality. Though invasive methods such as tissue biopsy are considered the gold standard for diagnosis and disease monitoring, they have several limitations. Therefore, there is an urgent need to identify and validate non-invasive biomarkers for the early diagnosis, prognosis, and treatment of lung cancer for improved patient management. Despite recent progress in the identification of non-invasive biomarkers, currently, there is a shortage of reliable and accessible biomarkers demonstrating high sensitivity and specificity for LC detection. In this review, we aim to cover the latest developments in the field, including the utility of biomarkers that are currently used in LC screening and diagnosis. We comment on their limitations and summarise the findings and developmental stages of potential molecular contenders such as microRNAs, circulating tumour DNA, and methylation markers. Furthermore, we summarise research challenges in the development of biomarkers used for screening purposes and the potential clinical applications of newly discovered biomarkers.
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Wang X, Yu N, Cheng G, Zhang T, Wang J, Deng L, Li J, Zhao X, Xu Y, Yang P, Bai N, Li Y, Bi N. Prognostic value of circulating tumour DNA during post-radiotherapy surveillance in locally advanced esophageal squamous cell carcinoma. Clin Transl Med 2022; 12:e1116. [PMID: 36437506 PMCID: PMC9702363 DOI: 10.1002/ctm2.1116] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/08/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The potential of circulating tumour DNA (ctDNA) as a reliable biomarker for relapse/metastasis early detection and prognosis in esophageal squamous cell carcinoma (ESCC) after radiotherapy/chemoradiotherapy (RT/CRT) initiation requires comprehensive investigation. METHODS Treatment-naive locally advanced ESCC patients with available baseline plasma samples were prospectively enrolled from November 2018 to January 2020. RT/CRT was delivered with a simultaneous integrated boost of radiation dose. Serial plasma samples were collected at baseline (T0 ), week 4 of RT/CRT (T1 ), 1-3 (T2 ) and 3-6 months post-RT/CRT (T3 ). ctDNA was analysed using next-generation sequencing of 474 cancer-relevant genes. RESULTS A total of 128 plasma samples from 40 eligible patients were analysed (median age: 64 [range: 40-78], 88% males, 95% stage III/IV), and the median follow-up time was 20.6 months (range: 12.2-33.3). During the post-RT/CRT surveillance including 36 patients, radiological progression was observed in 16 patients, and 69% (11/16) had detectable post-RT/CRT ctDNA prior to radiological progression, with a median lead time of 4.4 months compared with radiological imaging. ctDNA positivity at T1 (hazard ratio, HR: 3.60, 95% confidence interval, CI: 1.30-10.01) or T2 (HR: 5.45, 95% CI: 1.72-17.26) indicated inferior progression-free survival (PFS). ctDNA clearance between T0 -T1 (HR: 0.31, 95% CI: 0.08-1.13) or T0 -T2 (HR: 0.11; 95% CI: 0.02-0.61) was associated with relatively favourable PFS. Similar results were obtained when focusing on patients without esophagectomy after RT/CRT. Notably, detectable ctDNA at T1 was a potential indicator of high local recurrence risks (HR: 4.43, 95% CI: 1.31-15.04). CONCLUSIONS ctDNA was identified as a robust biomarker for early detection of disease progression and post-RT/CRT prognosis stratification in ESCC. Detectable ctDNA at week 4 of RT/CRT might indicate higher local recurrence risks, implying the potential clinical utility of ctDNA tests in guiding post-RT/CRT treatments for locoregional control in ESCC.
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Affiliation(s)
- Xin Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Nuo Yu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Guowei Cheng
- Department of Radiation OncologyCancer Hospital of HuanXingBeijingChina
| | - Tao Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jianyang Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lei Deng
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jiao Li
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiaotian Zhao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Yang Xu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Peng Yang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Na Bai
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.NanjingChina
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Nan Bi
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Yu Y, Ren Y, Fang J, Cao L, Liang Z, Guo Q, Han S, Ji Z, Wang Y, Sun Y, Chen Y, Li X, Xu H, Zhou J, Jiang L, Cheng Y, Han Z, Shi J, Chen G, Ma R, Fan Y, Sun S, Jiao L, Jia X, Wang L, Lu P, Xu Q, Luo X, Su W, Lu S. Circulating tumour DNA biomarkers in savolitinib-treated patients with non-small cell lung cancer harbouring MET exon 14 skipping alterations: a post hoc analysis of a pivotal phase 2 study. Ther Adv Med Oncol 2022; 14:17588359221133546. [PMID: 36339926 PMCID: PMC9629582 DOI: 10.1177/17588359221133546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/27/2022] [Indexed: 11/11/2022] Open
Abstract
Background Savolitinib, a selective MET inhibitor, showed efficacy in patients with non-small cell lung cancer (NSCLC), including pulmonary sarcomatoid carcinoma (PSC), harbouring MET exon 14 skipping alteration (METex14). Objective To analyse post hoc, the association between circulating tumour DNA (ctDNA) biomarkers and clinical outcomes, including resistance, with savolitinib. Design A multicentre, single-arm, open-label phase 2 study. Methods All enrolled patients with baseline plasma samples were included. Outcomes were objective response rate (ORR), progression-free survival (PFS) and overall survival (OS) by baseline METex14 and post-treatment clearance, coexisting gene alterations at baseline and disease progression. Results Among 66 patients with baseline ctDNA sequencing, 46 (70%) had detectable METex14. Frequent coexisting baseline gene alterations included TP53 and POT1 mutations. Patients with detectable baseline METex14 exhibited worse PFS [hazard ratio (HR), 1.77; 95% confidence interval (CI), 0.88-3.57; p = 0.108] and OS (HR, 3.26; 95% CI, 1.35-7.89; p = 0.006) than those without, despite showing a numerically higher ORR. Among 24 patients with baseline detectable METex14 and evaluable postbaseline samples, 13 achieved METex14 clearance post-treatment. Median time to first clearance was 1.3 months (range, 0.7-1.5). METex14 post-treatment clearance was associated with better ORR (92.3%; 95% CI, 64.0-99.8 versus 36.4%; 95% CI, 10.9-69.2; p = 0.0078), PFS (HR, 0.44; 95% CI, 0.2-1.3; p = 0.1225) and OS (HR, 0.31; 95% CI, 0.1-1.0; p = 0.0397) versus non-clearance. Among 22 patients with disease progression, 10 acquired pathway alterations (e.g. in RAS/RAF and PI3K/PTEN) alone or with secondary MET mutations (D1228H/N and Y1230C/H/S). Conclusion ctDNA biomarkers may allow for longitudinal monitoring of clinical outcomes with savolitinib in patients with METex14-positive PSC and other NSCLC subtypes. Specifically, undetectable baseline METex14 or post-treatment clearance may predict favourable clinical outcomes, while secondary MET mutations and other acquired gene alterations may explain resistance to savolitinib. Registration The trial was registered with ClinicalTrials.gov (NCT02897479) on 13 September 2016.
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Affiliation(s)
- Yongfeng Yu
- Department of Medical Oncology, Shanghai Chest
Hospital, Shanghai Jiaotong University, Shanghai, China
| | | | - Jian Fang
- Peking University Cancer Hospital and
Institute, Beijing, China
| | - Lejie Cao
- Anhui Provincial Hospital, The First Affiliated
Hospital of University of Science and Technology of China, Hefei,
China
| | - Zongan Liang
- West China Hospital of Sichuan University,
Chengdu, China
| | - Qisen Guo
- Shandong Cancer Hospital Affiliated to Shandong
University, Jinan, China
| | - Sen Han
- Peking University Cancer Hospital and
Institute, Beijing, China
| | - Zimei Ji
- Anhui Provincial Hospital, The First Affiliated
Hospital of University of Science and Technology of China, Hefei,
China
| | - Ye Wang
- West China Hospital of Sichuan University,
Chengdu, China
| | - Yulan Sun
- Shandong Cancer Hospital Affiliated to
Shandong University, Jinan, China
| | - Yuan Chen
- Tongji Hospital, Huazhong University of
Science and Technology, Wuhan, China
| | - Xingya Li
- The First Affiliated Hospital of Zhengzhou
University, Zhengzhou, China
| | - Hua Xu
- The Second Affiliated Hospital of Nanchang
University, Nanchang, China
| | - Jianying Zhou
- The First Affiliated Hospital of Zhejiang
University, Hangzhou, China
| | - Liyan Jiang
- Department of Medical Oncology, Shanghai Chest
Hospital, Shanghai Jiaotong University, Shanghai, China
| | | | - Zhigang Han
- The Affiliated Cancer Hospital of Xinjiang
Medical University, Urumqi, China
| | | | - Gongyan Chen
- Cancer Hospital of Harbin Medical University,
Harbin, China
| | - Rui Ma
- Liaoning Cancer Hospital, Shenyang,
China
| | - Yun Fan
- Zhejiang Cancer Hospital, Hangzhou,
China
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Lee HW, Kim E, Cho KJ, Park HJ, Seo J, Lee H, Baek E, Choi JR, Han KH, Lee ST, Park JY. Applications of molecular barcode sequencing for the detection of low-frequency variants in circulating tumour DNA from hepatocellular carcinoma. Liver Int 2022; 42:2317-2326. [PMID: 35776657 DOI: 10.1111/liv.15356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/02/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Liquid biopsy has emerged as a promising tool for minimally invasive and accurate detection of various malignancies. We aimed to apply molecular barcode sequencing to circulating tumour DNA (ctDNA) from liquid biopsies of hepatocellular carcinoma (HCC). STUDY DESIGN Patients with HCC or benign liver disease were enrolled between 2017 and 2018. Matched tissue and serum samples were obtained from these patients. Plasma cell-free DNA was extracted and subjected to targeted sequencing with ultra-high coverage and molecular barcoding. RESULTS The study included 143 patients: 102 with HCC, 7 with benign liver tumours and 34 with chronic liver disease. No tier 1/2 or oncogenic mutations were detected in patients with benign liver disease. Among the HCC patients, 49 (48%) had tier 1/2 mutations in at least one gene; detection rates were higher in advanced stages (75%) than in early stages (26%-33%). TERT was the most frequently mutated gene (30%), followed by TP53 (16%), CTNNB1 (14%), ARID2 (5%), ARID1A (4%), NFE2L2 (4%), AXIN1 (3%) and KRAS (1%). Survival among patients with TP53 mutations was significantly worse (p = 0.007) than among patients without these mutations, whereas CTNNB1 and TERT mutations did not affect survival. ctDNA testing combined with α-fetoprotein and prothrombin induced by vitamin K absence-II analyses improved HCC detection, even in early stages. CONCLUSIONS ctDNA detection using molecular barcoding technology offers dynamic and personalized information concerning tumour biology, such information can guide clinical diagnosis and management. This detection also has the potential as a minimally invasive approach for prognostic stratification and post-therapeutic monitoring.
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Affiliation(s)
- Hye Won Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea.,Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Esl Kim
- Department of Medical Science, The Graduate School, Yonsei University, Seoul, South Korea
| | - Kyung Joo Cho
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Hye Jung Park
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyeonah Lee
- Department of Medical Science, The Graduate School, Yonsei University, Seoul, South Korea
| | - Eunha Baek
- Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Kwang-Hyub Han
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Jun Yong Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea.,Yonsei Liver Center, Severance Hospital, Seoul, South Korea
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31
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Sauer CM, Heider K, Belic J, Boyle SE, Hall JA, Couturier D, An A, Vijayaraghavan A, Reinius MAV, Hosking K, Vias M, Rosenfeld N, Brenton JD. Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models. EMBO Mol Med 2022; 14:e15729. [PMID: 35694774 PMCID: PMC9358392 DOI: 10.15252/emmm.202215729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-genome sequencing (WGS) of circulating tumour DNA (ctDNA) is now a clinically important biomarker for predicting therapy response, disease burden and disease progression. However, the translation of ctDNA monitoring into vital preclinical PDX models has not been possible owing to low circulating blood volumes in small rodents. Here, we describe the longitudinal detection and monitoring of ctDNA from minute volumes of blood in PDX mice. We developed a xenograft Tumour Fraction (xTF) metric using shallow WGS of dried blood spots (DBS), and demonstrate its application to quantify disease burden, monitor treatment response and predict disease outcome in a preclinical study of PDX mice. Further, we show how our DBS-based ctDNA assay can be used to detect gene-specific copy number changes and examine the copy number landscape over time. Use of sequential DBS ctDNA assays could transform future trial designs in both mice and patients by enabling increased sampling and molecular monitoring.
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Affiliation(s)
- Carolin M Sauer
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Jelena Belic
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Samantha E Boyle
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James A Hall
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Medical Research Council Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Angela An
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Marika AV Reinius
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Karen Hosking
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Maria Vias
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James D Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
- Cambridge University Hospitals NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research CentreAddenbrooke's HospitalCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
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Gao Y, Zhao H, An K, Liu Z, Hai L, Li R, Zhou Y, Zhao W, Jia Y, Wu N, Li L, Ying J, Wang J, Xu B, Wu Z, Tong Z, He J, Sun Y. Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer. Clin Transl Med 2022; 12:e1014. [PMID: 35998020 PMCID: PMC9398227 DOI: 10.1002/ctm2.1014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Background Cancer cell–specific variation and circulating tumour DNA (ctDNA) methylation are promising biomarkers for non‐invasive cancer detection and molecular classification. Nevertheless, the applications of ctDNA to the early detection and screening of cancer remain highly challenging due to the scarcity of cancer cell–specific ctDNA, the low signal‐to‐noise ratio of DNA variation, and the lack of non‐locus‐specific DNA methylation technologies. Methods We enrolled three cohorts of breast cancer (BC) patients from two hospitals in China (BC: n = 123; healthy controls: n = 40). We developed a ctDNA whole‐genome bisulfite sequencing technology employing robust trace ctDNA capture from up to 200 μL plasma, mini‐input (1 ng) library preparation, unbiased genome‐wide coverage and comprehensive computational methods. Results A diagnostic signature comprising 15 ctDNA methylation markers exhibited high accuracy in the early (area under the curve [AUC] of 0.967) and advanced (AUC of 0.971) BC stages in multicentre patient cohorts. Furthermore, we revealed a ctDNA methylation signature that discriminates estrogen receptor status (Training set: AUC of 0.984 and Test set: AUC of 0.780). Different cancer types, including hepatocellular carcinoma and lung cancer, could also be well distinguished. Conclusions Our study provides a toolset to generate unbiased whole‐genome ctDNA methylomes with a minimal amount of plasma to develop highly specific and sensitive biomarkers for the early diagnosis and molecular subtyping of cancer.
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Affiliation(s)
- Yibo Gao
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ke An
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Renda Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weipeng Zhao
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Yongsheng Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lingyu Li
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Jianming Ying
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Jie He
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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Bregni G, Pretta A, Senti C, Acedo Reina E, Vandeputte C, Trevisi E, Gkolfakis P, Kehagias P, Deleporte A, Van Laethem JL, Vergauwe P, Van den Eynde M, Deboever G, Janssens J, Demolin G, Holbrechts S, Clausse M, De Grez T, Peeters M, D'Hondt L, Geboes K, Besse-Hammer T, Rothé F, Flamen P, Hendlisz A, Sclafani F. Circulating DNA in the neoadjuvant setting of early stage colon cancer. Acta Oncol 2022; 61:1223-1229. [PMID: 35866544 DOI: 10.1080/0284186x.2022.2101023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND While circulating tumour (ct)DNA is an indicator of minimal residual disease and negative prognostic factor in stage II-III colon cancer, no study has ever analysed the value of this biomarker in colon cancer patients treated with neoadjuvant chemotherapy. We sought to fill this gap by using prospectively collected plasma samples from 80 stage III colon cancer patients, receiving one cycle of neoadjuvant FOLFOX followed by surgery +/- adjuvant FOLFOX in the PePiTA trial. MATERIAL AND METHODS Samples were collected at baseline, 2 weeks and surgery. NPY and WIF1 were selected as universal methylation markers for ctDNA, and analysed with ddPCR technology. ROC curves were applied for cut-off points, and outcome measures included 5-year disease-free survival (DFS) and 6-year overall survival (OS). RESULTS After a median follow-up of 52.5 months, baseline circulating-free (cf) DNA was an independent prognostic factor for DFS (HR 3.35, 95% CI: 1.15-9.77, p = .03), and a trend towards a similar association was observed for relative cfDNA changes between baseline and surgery (HR 2.57, 95% CI: 0.94-7.05, p = .07). Among 60 ctDNA assessable patients, 25 (42%) had detectable ctDNA at baseline. While detection of ctDNA at any pre-operative timepoint was not associated with outcome, patients with ctDNA increase (change of the worst trending methylation marker ≥11%, or mean ctDNA change of NPY and WIF1 ≥ 0%) between baseline and surgery showed a trend towards worse 5-year DFS (HR 3.66, 95% CI: 0.81-16.44, p = .09). CONCLUSION This is the first study of ctDNA in the neoadjuvant setting of early-stage colon cancer. Results are hypothesis-generating and should be confirmed in larger series.
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Prakash N, Pradeep GL. Circulating biomarkers in oral cancer: Unravelling the mystery. J Oral Maxillofac Pathol 2022; 26:300-306. [PMID: 36588829 PMCID: PMC9802512 DOI: 10.4103/jomfp.jomfp_338_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 01/03/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is among the most common malignancies and a leading cause of death in developing countries. Late diagnosis and regional and/or distant metastasis worsen the prognosis of this condition. Despite the advances in diagnostic modalities and management strategies, there is little improvement in the 5-year survival rate. A deeper insight into the molecular events of various tumours has enabled the use of minimally invasive methods for monitoring disease progression, prognostication and treatment monitoring. Although studies in OSCC are preliminary, the use of liquid biopsies has opened new frontiers for the development of biomarkers that can serve as alternatives to conventional biopsies and imaging methods. Circulating biomarkers in blood allow for the real-time monitoring of tumour and therapeutic responses. This review aims to outline the promises and challenges of circulating biomarkers in OSCC with special emphasis on circulating tumour cells, circulating tumor DNA, and exosomes.
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Affiliation(s)
- Nilima Prakash
- Department of Oral Pathology and Microbiology, MGV's KBH Dental College and Hospital, Nashik, Maharashtra, India
| | - GL Pradeep
- Department of Oral Pathology and Microbiology, MGV's KBH Dental College and Hospital, Nashik, Maharashtra, India
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Cabezas-Camarero S, García-Barberán V, Pérez-Alfayate R, Casado-Fariñas I, Sloane H, Jones FS, Pérez-Segura P. Detection of IDH1 Mutations in Plasma Using BEAMing Technology in Patients with Gliomas. Cancers (Basel) 2022; 14:cancers14122891. [PMID: 35740557 PMCID: PMC9221506 DOI: 10.3390/cancers14122891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary In contrast with other solid tumors, only a few, small studies have shown the feasibility of detecting different biomarkers in the peripheral blood (PB) of patients with gliomas. A prospective study was conducted, enrolling 10 patients with gliomas where 33 consecutive PB samples were analyzed. Among the six patients with isocitrate dehydrogenase 1 (IDH1)-mutant tumors that were surveyed, circulating tumor DNA (ctDNA) was detected in PB in three of them (50%), at timepoints at which the patients were either untreated or exhibited progressive disease. While no false positives were identified, the false-negative rate was high, reaching 86% (18/21). Finally, in one of the IDH1-mutant cases, the Beads, Emulsion, Amplification and Magnetics (BEAMing) digital PCR technology detected one of the two IDH1 mutations that had been detected in the patient’s tumor sample in plasma, 7 years prior to its detection in blood. Abstract Molecular testing using blood-based liquid biopsy approaches has not been widely investigated in patients with glioma. A prospective single-center study enrolled patients with gliomas ranging from grade II to IV. Peripheral blood (PB) was drawn at different timepoints for circulating tumour DNA (ctDNA) monitoring. Next-generation sequencing (NGS) was used for the study of isocitrate dehydrogenase 1 (IDH1) mutations in the primary tumor. Beads, Emulsion, Amplification and Magnetics (BEAMing) was used for the study of IDH1 mutations in plasma and correlated with the NGS results in the tumor. Between February 2017 and July 2018, ten patients were enrolled, six with IDH1-mutant and four with IDH1 wild-type gliomas. Among the six IDH-mutant gliomas, three had the same IDH1 mutation detected in plasma (50%), and the IDH1-positive ctDNA result was obtained in patients either at diagnosis (no treatment) or during progressive disease. While the false-negative rate reached 86% (18/21), 15 out of the 18 (83%) plasma-negative results were from PB collected from the six IDH-mutant patients at times at which there was no accompanying evidence of tumor progression, as assessed by MRI. There were no false-positive cases in plasma collected from patients with IDH1 wild-type tumors. BEAMing detected IDH1 mutations in the plasma of patients with gliomas, with a modest clinical sensitivity (true positivity rate) but with 100% clinical specificity, with complete agreement between the mutant loci detected in tumor and plasma. Larger prospective studies should be conducted to expand on these findings, and further explore the clearance of mutations in PB from IDH1-positive patients in response to therapy.
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Affiliation(s)
- Santiago Cabezas-Camarero
- Head & Neck Cancer, Neuro-Oncology and Genetic Counseling Unit, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, Paseo del Profesor Martín Lagos S/N, 28040 Madrid, Spain;
- Correspondence: ; Tel.: +34-91-330-3000
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, 28040 Madrid, Spain;
| | - Rebeca Pérez-Alfayate
- Department of Neurosurgery, Hospital Clínico Universitario San Carlos, 28040 Madrid, Spain;
| | - Isabel Casado-Fariñas
- Pathology Department, Hospital Clínico Universitario San Carlos, 28040 Madrid, Spain;
| | - Hillary Sloane
- Medical affairs Division, Sysmex Inostics, Inc., Baltimore, MD 21205, USA; (H.S.); (F.S.J.)
| | - Frederick S. Jones
- Medical affairs Division, Sysmex Inostics, Inc., Baltimore, MD 21205, USA; (H.S.); (F.S.J.)
| | - Pedro Pérez-Segura
- Head & Neck Cancer, Neuro-Oncology and Genetic Counseling Unit, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, Paseo del Profesor Martín Lagos S/N, 28040 Madrid, Spain;
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Gilson P, Merlin JL, Harlé A. Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers (Basel) 2022; 14:1384. [PMID: 35326534 DOI: 10.3390/cancers14061384] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Most malignant tumours are highly heterogeneous at molecular and phenotypic levels. Tumour variability poses challenges for the management of patients, as it arises between patients and even evolves in space and time within a single patient. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of tumour diversity in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate tumour heterogeneity. Abstract Human solid malignancies harbour a heterogeneous set of cells with distinct genotypes and phenotypes. This heterogeneity is installed at multiple levels. A biological diversity is commonly observed between tumours from different patients (inter-tumour heterogeneity) and cannot be fully captured by the current consensus molecular classifications for specific cancers. To extend the complexity in cancer, there are substantial differences from cell to cell within an individual tumour (intra-tumour heterogeneity, ITH) and the features of cancer cells evolve in space and time. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity with an emphasis on ITH and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of ITH in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate ITH.
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Lyskjær I, Davies C, Strobl A, Hindley J, James S, Lalam RK, Cross W, Hide G, Rankin KS, Jeys L, Tirabosco R, Stevenson J, O’Donnell P, Cool P, Flanagan AM. Circulating tumour DNA is a promising biomarker for risk stratification of central chondrosarcoma with IDH1/2 and GNAS mutations. Mol Oncol 2021; 15:3679-3690. [PMID: 34528398 PMCID: PMC8637565 DOI: 10.1002/1878-0261.13102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Chondrosarcoma (CS) is a rare tumour type and the most common primary malignant bone cancer in adults. The prognosis, currently based on tumour grade, imaging and anatomical location, is not reliable, and more objective biomarkers are required. We aimed to determine whether the level of circulating tumour DNA (ctDNA) in the blood of CS patients could be used to predict outcome. In this multi-institutional study, we recruited 145 patients with cartilaginous tumours, of which 41 were excluded. ctDNA levels were assessed in 83 of the remaining 104 patients, whose tumours harboured a hotspot mutation in IDH1/2 or GNAS. ctDNA was detected pre-operatively in 31/83 (37%) and in 12/31 (39%) patients postoperatively. We found that detection of ctDNA was more accurate than pathology for identification of high-grade tumours and was associated with a poor prognosis; ctDNA was never associated with CS grade 1/atypical cartilaginous tumours (ACT) in the long bones, in neoplasms sited in the small bones of the hands and feet or in tumours measuring less than 80 mm. Although the results are promising, they are based on a small number of patients, and therefore, introduction of this blood test into clinical practice as a complementary assay to current standard-of-care protocols would allow the assay to be assessed more stringently and developed for a more personalised approach for the treatment of patients with CS.
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Affiliation(s)
- Iben Lyskjær
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Medical Genomics Research GroupUniversity College LondonUCL Cancer InstituteLondonUK
| | - Christopher Davies
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Anna‐Christina Strobl
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Joanna Hindley
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Steven James
- Department of Musculoskeletal ImagingRoyal Orthopaedic HospitalBirminghamUK
| | - Radhesh K. Lalam
- Department of RadiologyRoyal National Orthopaedic HospitalStanmoreUK
| | - William Cross
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
| | - Geoff Hide
- North of England Bone and Soft Tissue Tumour ServiceFreeman HospitalNewcastleUK
| | - Kenneth S. Rankin
- North of England Bone and Soft Tissue Tumour ServiceFreeman HospitalNewcastleUK
- Newcastle Centre for CancerNewcastle UniversityUK
| | - Lee Jeys
- Orthopaedic DepartmentRoyal Orthopaedic Hospital NHS Foundation TrustBirminghamUK
| | - Roberto Tirabosco
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Jonathan Stevenson
- Department of Orthopaedic Oncology and ArthroplastyRoyal Orthopaedic Hospital NHS Foundation TrustBirminghamUK
| | | | - Paul O’Donnell
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of RadiologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Paul Cool
- Robert Jones & Agnes Hunt Orthopaedic Hospital NHS Foundation TrustOswestryUK
- Keele UniversityUK
| | - Adrienne M. Flanagan
- Research Department of PathologyUniversity College LondonUCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
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Ji H, Long X, Gu J, Jin J, Mao X, Wang Z, Ma H, Chen L. Longitudinal Monitoring of Plasma Circulating Tumour DNA Enables the Prediction of Early Relapse in Patients with Non-Hodgkin Lymphoma: A Case Series. Diagnostics (Basel) 2021; 11:diagnostics11112055. [PMID: 34829401 PMCID: PMC8618087 DOI: 10.3390/diagnostics11112055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 01/09/2023] Open
Abstract
Growing evidence now suggests that circulating tumour DNA (ctDNA) has great potential as a non-invasive biomarker for disease monitoring, since ctDNA carries tumour-specific modifications. In particular, monitoring ctDNA has important implications for identifying patients with haematological malignancies at clinical risk of disease progression. We hereby describe three patients with B-cell non-Hodgkin lymphoma and investigate the clinical value of sequential ctDNA profiling for the early detection of tumour relapse. Somatic mutations in diagnostic tumour biopsy samples of these three patients were identified by applying high-throughput next-generation sequencing. Droplet digital PCR probes and primers were designed and tested for each hotspot mutation. Serial ctDNA analysis was subsequently conducted among these three patients. We found that the longitudinal monitoring of plasma ctDNA could predict for at least one month in advance compared with flow cytometry, cytology and conventional imaging modalities. Therefore, our results support liquid biopsy based on ctDNA as a non-invasive complementary modality to other detection methods for detecting early relapse and contribute to more precise management for non-Hodgkin lymphoma patients.
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Affiliation(s)
- Hongyan Ji
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Xiaolu Long
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Jia Gu
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Jin Jin
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Xia Mao
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Zhiqiong Wang
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Heng Ma
- FNA Cytology Examining Room, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Liting Chen
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
- Correspondence:
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Zhang S, Zhang T, Liu H, Zhao J, Zhou H, Su X, Liu X, Li L, Qiu L, Qian Z, Zhou S, Gong W, Meng B, Ren X, He J, Wang X, Zhang H. Tracking the evolution of untreated high-intermediate/high-risk diffuse large B-cell lymphoma by circulating tumour DNA. Br J Haematol 2021; 196:617-628. [PMID: 34664256 DOI: 10.1111/bjh.17894] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/25/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a highly heterogenous malignancy, early identification of patients for relapse remains challenging. The potential to non-invasively monitor tumour evolutionary dynamics of DLBCL needs to be further established. In the present study, 17 tumour biopsy and 38 plasma samples from 38 patients with high-intermediate/high-risk DLBCL were evaluated at baseline. Longitudinal blood samples were also collected during therapy. Circulating tumour DNA (ctDNA) was analysed using targeted sequencing based on a gene panel via a recently developed methodology, circulating single-molecule amplification and re-sequencing technology (cSMART). We found that the most frequently mutated genes were tumour protein p53 (TP53; 42·1%), histone-lysine N-methyltransferase 2D (KMT2D; 28·9%), caspase recruitment domain family member 11 (CARD11; 21·1%), cAMP response element-binding protein binding protein (CREBBP; 15·8%), β2 -microglobulin (B2M; 15·8%), and tumour necrosis factor alpha-induced protein 3 (TNFAIP3; 15·8%). The mutation profiles between ctDNA and matched tumour tissue showed good concordance; however, more mutation sites were detected in ctDNA samples. Either TP53 or B2M mutations before treatment predicted poor prognosis. Analysis of dynamic blood samples confirmed the utility of ctDNA for the real-time assessment of treatment response and revealed that the increases in ctDNA levels and changes in KMT2D mutation status could be useful predictors of disease progression. Our present results suggest that ctDNA is a promising method for the detection of mutation spectrum and serves as a biomarker for disease monitoring and predicting clinical recurrence.
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Affiliation(s)
- Sicong Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Tingting Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Hengqi Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jing Zhao
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | | | | | - Xianming Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lanfang Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lihua Qiu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Zhengzi Qian
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Shiyong Zhou
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Wenchen Gong
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bin Meng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiubao Ren
- Department of Immunology/Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jin He
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
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Månsson CT, Vad-Nielsen J, Meldgaard P, Nielsen AL, Sorensen BS. EGFR transcription in non-small-cell lung cancer tumours can be revealed in ctDNA by cell-free chromatin immunoprecipitation (cfChIP). Mol Oncol 2021; 15:2868-2876. [PMID: 34453867 PMCID: PMC8564636 DOI: 10.1002/1878-0261.13093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
Determination of tumour‐specific transcription based on liquid biopsies possesses a large diagnostic and prognostic potential in non‐small cell lung cancer (NSCLC). Cell‐free DNA (cfDNA) packed in nucleosomes mirrors the histone modification profiles present in the cells of origin. H3 lysine 36 trimethylation (H3K36me3)‐modified nucleosomes are associated with active genes, and therefore, cell‐free chromatin immunoprecipitation (cfChIP) of H3K36me3‐associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates. We hypothesized that cfChIP can delineate transcriptional status of genes harbouring somatic cancer mutations and analysed the recurrently observed EGFR‐L858R mutation as an example. In representative NSCLC cell lines, the relationship between wild‐type (WT) and mutated EGFR transcriptional activity and mRNA expression levels was analysed using H3K36me3 ChIP and EGFR mRNA reverse transcription quantitative PCR (RT‐qPCR), respectively. The ChIP analysis showed that both WT and mutated EGFR are transcribed and that mRNA is similarly expressed per EGFR copy. Based on this observation, we proceeded with EGFR cfChIP using blood plasma from NSCLC patients harbouring the EGFR‐L858R mutation. EGFR‐WT fragments can originate from both nontumour cells with no or low EGFR transcription and tumour cells with active EGFR transcription, whereas EGFR‐L858R fragments must specifically originate from tumour cells. H3K36me3 cfChIP followed by droplet digital PCR (ddPCR) revealed significantly higher enrichment of EGFR‐L858R compared to EGFR‐WT fragments. This is in alignment with EGFR‐L858R being actively transcribed in the NSCLC tumour cells. This study is proof‐of‐principle that cfChIP can be used to identify tumour‐specific transcriptional activity of mutated alleles, which can expand the utility of liquid biopsy‐based cfDNA analyses to enhance tumour diagnostics and therapeutics.
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Alcoceba M, García-Álvarez M, Chillón MC, Jiménez C, Medina A, Antón A, Blanco O, Díaz LG, Tamayo P, González-Calle V, Vidal MJ, Cuello R, Díaz Gálvez FJ, Queizán JA, Martín A, González M, García-Sanz R, Sarasquete ME. Liquid biopsy: a non-invasive approach for Hodgkin lymphoma genotyping. Br J Haematol 2021; 195:542-551. [PMID: 34312841 DOI: 10.1111/bjh.17719] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022]
Abstract
The Hodgkin lymphoma (HL) genomic landscape is hardly known due to the scarcity of tumour cells in the tissue. Liquid biopsy employing circulating tumour DNA (ctDNA) can emerge as an alternative tool for non-invasive genotyping. By using a custom next generation sequencing (NGS) panel in combination with unique molecule identifiers, we aimed to identify somatic variants in the ctDNA of 60 HL at diagnosis. A total of 277 variants were detected in 36 of the 49 samples (73·5%) with a good quality ctDNA sample. The median number of variants detected per patient was five (range 1-23) with a median variant allele frequency of 4·2% (0·84-28%). Genotyping revealed somatic variants in the following genes: SOCS1 (28%), IGLL5 (26%), TNFAIP3 (23%), GNA13 (23%), STAT6 (21%) and B2M (19%). Moreover, several poor prognosis features (high LDH, low serum albumin, B-symptoms, IPI ≥ 3 or at an advanced stage) were related to significantly higher amounts of ctDNA. Variant detection in ctDNA by NGS is a feasible approach to depict the genetic features of HL patients at diagnosis. Our data favour the implementation of liquid biopsy genotyping for the routine evaluation of HL patients.
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Affiliation(s)
- Miguel Alcoceba
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - María García-Álvarez
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - M Carmen Chillón
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Cristina Jiménez
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Alejandro Medina
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Alicia Antón
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Oscar Blanco
- Department of Pathology, University Hospital of Salamanca (HUS/IBSAL), Spain
| | - Luis G Díaz
- Department of Nuclear Medicine, University Hospital of Salamanca (HUS/IBSAL),, Salamanca, Spain
| | - Pilar Tamayo
- Department of Nuclear Medicine, University Hospital of Salamanca (HUS/IBSAL),, Salamanca, Spain
| | - Verónica González-Calle
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | | | - Rebeca Cuello
- Department of Hematology, University Hospital of Valladolid,, Valladolid, Spain
| | | | | | - Alejandro Martín
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Marcos González
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - Ramón García-Sanz
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
| | - M Eugenia Sarasquete
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Spain
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Moretto R, Rossini D, Capone I, Boccaccino A, Perrone F, Tamborini E, Masi G, Antoniotti C, Marmorino F, Conca V, Borelli B, Martignetti A, Pecora I, Simionato F, Cupini S, Ambrosini M, Manca P, Pietrantonio F, Falcone A, Cremolini C. Rationale and Study Design of the PARERE Trial: Randomized phase II Study of Panitumumab Re-Treatment Followed by Regorafenib Versus the Reverse Sequence in RAS and BRAF Wild-Type Chemo-Refractory Metastatic Colorectal Cancer Patients. Clin Colorectal Cancer 2021; 20:314-317. [PMID: 34364814 DOI: 10.1016/j.clcc.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/05/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND A recent phase II randomized Japanese study reported better survival with regorafenib followed at progression by cetuximab ± irinotecan compared with the reverse standard sequence in chemo-refractory and anti-EGFR-naïve, RAS wild-type (wt) mCRC patients. Nowadays the use of anti-EGFR antibodies is more frequently anticipated to the first-line of therapy especially in patients with left-sided RAS/BRAF wt tumours. However, retrospective analyses and phase II single-arm trials showed promising activity of re-using anti-EGFRs in metastatic colorectal cancer (mCRC) patients who previously achieved benefit from a first-line anti-EGFR-based treatment. Post-hoc analyses of these trials revealed that the detection of RAS mutations in circulating tumour DNA (ct-DNA) at the time of re-treatment may be useful to identify resistant patients. PATIENTS AND METHODS PARERE (NCT04787341) is a prospective, open label, multicentre phase II study in which 214 RAS/BRAF wt chemo-refractory mCRC patients with previous benefit from first-line anti-EGFR-based treatment and RAS/BRAF wt ct-DNA in the liquid biopsy collected at the time of inclusion will be randomized in a 1:1 ratio to receive panitumumab followed after progression by regorafenib versus the reverse sequence. Primary endpoint is overall survival. Secondary endpoints are 1st-progression free-survival (PFS), 2nd-PFS, time to failure strategy, objective response rate, and safety. AIM OF THE STUDY The aim of this study is to validate the role of anti-EGFR retreatment and its proper placement in the therapeutic route of mCRC patients selected according to the analysis of ct-DNA in liquid biopsy. Results are expected at the end of 2023.
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Affiliation(s)
- Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Daniele Rossini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Iolanda Capone
- Laboratory of Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandra Boccaccino
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federica Perrone
- Laboratory of Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Elena Tamborini
- Laboratory of Molecular Pathology, Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Gianluca Masi
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Carlotta Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federica Marmorino
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Veronica Conca
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Beatrice Borelli
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Irene Pecora
- Division of Medical Oncology, Misericordia General Hospital, Grosseto, Italy
| | - Francesca Simionato
- Department of Oncology, San Bortolo General Hospital, ULSS 8 Berica, Vicenza, Italy
| | - Samanta Cupini
- Department of Oncology, Division of Medical Oncology, Azienda Toscana Nord Ovest, Livorno, Italy
| | - Margherita Ambrosini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Manca
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Oncology and Hemato-Oncology Department, University of Milan, Milan, Italy
| | - Alfredo Falcone
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technology in Medicine and Surgery, University of Pisa, Pisa, Italy.
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Relton A, Collins A, Guttery DS, Gorsia DN, McDermott HJ, Moss EL. Patient acceptability of circulating tumour DNA testing in endometrial cancer follow-up. Eur J Cancer Care (Engl) 2021; 30:e13429. [PMID: 33616269 DOI: 10.1111/ecc.13429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/15/2020] [Accepted: 01/11/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Circulating tumour DNA (ctDNA) is emerging as a potential option to detect disease recurrence in many cancer types, however, ensuring patient acceptability of changing clinical practice and the introduction of new technology is paramount. METHODS Patients enrolled in a non-intervention cohort study determining the ability of ctDNA to detect recurrent endometrial cancer (EC) were invited to participate in a semi-structured interview. Analysis was performed by Template Analysis. RESULTS Eighteen patients were interviewed. A ctDNA blood test was viewed by participants as more physically and psychologically acceptable than clinical examination to monitor for EC recurrence. In particular, participants expressed overwhelming preference for a blood test rather than pelvic examination. Although participants acknowledged that an abnormal ctDNA result could cause anxiety, they expressed a preference to be informed of their results, even if a recurrence was too small to detect radiologically. Explanations for these opinions were a desire for certainty whether their cancer would recur or not, and knowledge would help them be more aware of symptoms that should be reported to their clinician. CONCLUSIONS ctDNA monitoring to identify EC recurrence appears to be acceptable to patients, and for many, it may be preferable to clinical examination.
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Affiliation(s)
- Anna Relton
- School of Sport, Exercise and Health Sciences, National Centre for Sport and Exercise Medicine, Loughborough University, Loughborough, Leicestershire, UK
| | - Anna Collins
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Diviya N Gorsia
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hilary J McDermott
- School of Sport, Exercise and Health Sciences, National Centre for Sport and Exercise Medicine, Loughborough University, Loughborough, Leicestershire, UK
| | - Esther L Moss
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
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Collins A, Taylor A, Guttery DS, Moss EL. Innovative Follow-up Strategies for Endometrial Cancer. Clin Oncol (R Coll Radiol) 2021; 33:e383-e392. [PMID: 34172343 DOI: 10.1016/j.clon.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/26/2021] [Accepted: 06/01/2021] [Indexed: 01/22/2023]
Abstract
Increasing recognition of the heterogeneous nature of endometrial cancer, the excellent prognosis of low-risk cases and improvements in risk stratification offer opportunities for innovative, personalised follow-up strategies. This review article outlines the evidence base for alternative follow-up strategies in the different risk categories of endometrial cancer, cancer survivorship programmes and considers future directions in endometrial cancer follow-up, including emerging new techniques, such as the liquid biopsy, and opportunities for combining molecular and clinicopathological features to personalise endometrial cancer follow-up.
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Affiliation(s)
- A Collins
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - A Taylor
- Royal Marsden NHS Foundation Trust, London, UK
| | - D S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - E L Moss
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
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Wang J, Wang J, Wang J, Qian Z, Xu W, Hang X. Combination treatment for advanced hepatocellular carcinoma with portal vein tumour thrombus: A case report. J Int Med Res 2021; 49:300060521994406. [PMID: 33596694 PMCID: PMC7897824 DOI: 10.1177/0300060521994406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We present a case of a 43-year-old man with advanced hepatocellular carcinoma (HCC) with portal vein tumour thrombus. Initially, transcatheter arterial chemoembolization (TACE) was performed. Although alpha-fetoprotein (AFP) levels decreased, circulating tumour DNA (ctDNA) levels showed an upward trend, and abdominal magnetic resonance imaging (MRI) showed that tumours in the portal vein had increased. Based on ctDNA profiling, apatinib and anti-programmed cell death protein 1 (anti-PD-1) antibodies and were sequentially administered. Approximately three months later, intrahepatic tumours had significantly diminished and AFP and ctDNA levels had reduced. The response was sustained at the 23-month follow-up and the patient was in good health. Combination treatment of TACE, apatinib and anti-PD-1 antibodies was effective, and profiling of ctDNA fragmentation may be beneficial in the therapeutic management of patients with HCC.
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Affiliation(s)
- Jianrong Wang
- Department of Infectious Diseases, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junxue Wang
- Department of Infectious Diseases, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jianzhu Wang
- Pharmaceutical College of Taizhou Vocational and Technical College, Taizhou, China
| | - Ziliang Qian
- Prophet Genomics Inc, 1229 Briarcreekct, San Jose, CA, USA
| | - Wensheng Xu
- Department of Infectious Diseases, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xiaofeng Hang
- Department of Infectious Diseases, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Escudero L, Martínez-Ricarte F, Seoane J. ctDNA-Based Liquid Biopsy of Cerebrospinal Fluid in Brain Cancer. Cancers (Basel) 2021; 13:1989. [PMID: 33919036 DOI: 10.3390/cancers13091989] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
The correct characterisation of central nervous system (CNS) malignancies is crucial for accurate diagnosis and prognosis and also the identification of actionable genomic alterations that can guide the therapeutic strategy. Surgical biopsies are performed to characterise the tumour; however, these procedures are invasive and are not always feasible for all patients. Moreover, they only provide a static snapshot and can miss tumour heterogeneity. Currently, monitoring of CNS cancer is performed by conventional imaging techniques and, in some cases, cytology analysis of the cerebrospinal fluid (CSF); however, these techniques have limited sensitivity. To overcome these limitations, a liquid biopsy of the CSF can be used to obtain information about the tumour in a less invasive manner. The CSF is a source of cell-free circulating tumour DNA (ctDNA), and the analysis of this biomarker can characterise and monitor brain cancer. Recent studies have shown that ctDNA is more abundant in the CSF than plasma for CNS malignancies and that it can be sequenced to reveal tumour heterogeneity and provide diagnostic and prognostic information. Furthermore, analysis of longitudinal samples can aid patient monitoring by detecting residual disease or even tracking tumour evolution at relapse and, therefore, tailoring the therapeutic strategy. In this review, we provide an overview of the potential clinical applications of the analysis of CSF ctDNA and the challenges that need to be overcome in order to translate research findings into a tool for clinical practice.
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Keegan NM, Furney SJ, Walshe JM, Gullo G, Kennedy MJ, Smith D, McCaffrey J, Kelly CM, Egan K, Kerr J, Given M, O'Donovan P, Hernando A, Teiserskiene A, Parker I, Kay E, Farrelly A, Carr A, Calzaferri G, McDermott R, Keane MM, Grogan L, Breathnach O, Morris PG, Toomey S, Hennessy BT. Phase Ib Trial of Copanlisib, A Phosphoinositide-3 Kinase (PI3K) Inhibitor, with Trastuzumab in Advanced Pre-Treated HER2-Positive Breast Cancer "PantHER". Cancers (Basel) 2021; 13:1225. [PMID: 33799597 DOI: 10.3390/cancers13061225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Patients with HER-2 positive breast cancer who progress through available HER2-targeted therapy, at present, have few effective treatment options. PIK3CA is mutated in approximately 20% of HER2 positive breast cancers, contributes to HER-2 therapy resistance and may be predictive of response to PI3K inhibitors, including copanlisib. PIK3CA gene mutations were assessed in archival tumour tissue and serially in plasma circulating tumour DNA over the course of treatment with copanlisib. Disease stabilisation (stable disease ≥16 weeks) was seen with copanlisib and trastuzumab in a proportion of participants (n = 6, 50%). PIK3CA mutation detected in archival tumour tissue did not appear to predict tumour response to copanlisib and trastuzumab in this small, heavily pre-treated cohort. Notably, PIK3CA circulating tumour DNA mutations were detected in the plasma of all trial participants, including those who tested negative for the mutation in tissue. This study established a dosing strategy for the novel combination of the PI3K inhibitor copanlisib with trastuzumab and suggested clinical activity for the combination in heavily pre-treated HER-2 positive advanced breast cancer. Further evaluation in a phase 2 study in patients with HER2 therapy resistant tumours is ongoing (NCT02705859). Abstract Background: Activation of the phosphoinositide-3 kinase (PI3K) pathway is a resistance mechanism to anti-human epidermal growth factor receptor 2 (HER2) therapy. This phase Ib trial was conducted to determine the maximum tolerated dose (MTD) of copanlisib, an intravenous (IV) pan-class I PI3K inhibitor, combined with trastuzumab. Methods: Patients with advanced HER2-positive breast cancer and disease progression following at least one prior line of HER2 therapy in the metastatic setting were treated with copanlisib (45 or 60 mg) IV on days 1, 8 and 15 of a 28-day cycle with a fixed dose of trastuzumab 2 mg/kg weekly. Results: Twelve patients were enrolled. The MTD was determined as copanlisib 60 mg plus trastuzumab 2 mg/kg weekly. The most common adverse events of any grade occurring in more than two patients were hyperglycaemia (58%), fatigue (58%), nausea (58%) and hypertension (50%). Stable disease was confirmed at 16 weeks in six participants (50%). PIK3CA mutations were detected in archival tumour of six participants (50%). PIK3CA hotspot mutations, were detectable in pre- and on-treatment plasma of all participants. Pre- and post-treatment tumour biopsies for two patients identified temporal genomic heterogeneity, somatic mutations in the TRRAP gene, which encodes a PI3K-like protein kinase, and emergent somatic mutations related to protein kinase signalling. Conclusion: Copanlisib and trastuzumab can be safely administered with fair overall tolerability. Preliminary evidence of tumour stability was observed in patients with heavily pre-treated, metastatic HER2 positive breast cancer. Several potential biomarkers were identified for further study in the current phase 2 clinical trial. NCT: 02705859.
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Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. Epigenomes 2021; 5:6. [PMID: 33777442 PMCID: PMC7610445 DOI: 10.3390/epigenomes5010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples. METHODS For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls. RESULTS Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot. CONCLUSIONS The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types.
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Affiliation(s)
- Celina Whalley
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Karl Payne
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Enric Domingo
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Andrew Blake
- Department of Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (E.D.); (A.B.)
| | - Susan Richman
- Pathology and Data Analytics, Leeds Institute of Medical Research, St James University Hospital, Leeds LS2 9JT, UK;
| | - Jill Brooks
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Nikolaos Batis
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Rachel Spruce
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | | | - Hisham Mehanna
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Paul Nankivell
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
| | - Andrew D. Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK; (C.W.); (K.P.); (J.B.); (N.B.); (R.S.); (H.M.); (P.N.)
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Stergiopoulou D, Markou A, Tzanikou E, Ladas I, Makrigiorgos GM, Georgoulias V, Lianidou E. ESR1 NAPA Assay: Development and Analytical Validation of a Highly Sensitive and Specific Blood-Based Assay for the Detection of ESR1 Mutations in Liquid Biopsies. Cancers (Basel) 2021; 13:556. [PMID: 33535614 DOI: 10.3390/cancers13030556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary A considerable number of estrogen-receptor–positive (ER+) breast cancer patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. In the present study, we developed and analytically validated a novel, highly sensitive and specific nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO)-assisted Amplification refractory mutation system (ARMS) (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G). The assay was further applied in 13 ER+ breast cancer (BrCa) primary tumour tissues (FFPEs), 13 non-cancerous breast tissues (mammoplasties), and 32 pairs of liquid biopsy samples [circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA)] obtained at different time points from 8 ER+ metastatic breast cancer patients. In the plasma ctDNA, the ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected during the follow-up period at five consecutive time points in one patient. In the CTCs, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low-cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. Abstract A considerable number of estrogen receptor-positive breast cancer (ER+ BrCa) patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. We developed and analytically validated a highly sensitive and specific NaME-PrO-assisted ARMS (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G) in circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA) in patients with ER+ BrCa. The analytical specificity, analytical sensitivity and reproducibility of the assay were validated using synthetic oligos standards. We further applied the developed ESR1 NAPA assay in 13 ER+ BrCa primary tumour tissues, 13 non-cancerous breast tissues (mammoplasties) and 64 liquid biopsy samples: 32 EpCAM-positive cell fractions and 32 paired plasma ctDNA samples obtained at different time points from 8 ER+ metastatic breast cancer patients, during a 5-year follow-up period. Peripheral blood from 11 healthy donors (HD) was used as a control. The developed assay is highly sensitive (a detection of mutation-allelic-frequency (MAF) of 0.5% for D538G and 0.1% for Y537S, Y537C, Y537N), and highly specific (0/13 mammoplasties and 0/11 HD for all mutations). In the plasma ctDNA, ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected in five sequential ctDNA samples during the follow-up period in the same patient. In the EpCAM-isolated cell fractions, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. The clinical performance of the ESR1 NAPA assay will be prospectively evaluated in a large number of well-characterized patient cohorts.
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Shah D, Lamarca A, Valle JW, McNamara MG. The Potential Role of Liquid Biopsies in Advancing the Understanding of Neuroendocrine Neoplasms. J Clin Med 2021; 10:jcm10030403. [PMID: 33494364 PMCID: PMC7865482 DOI: 10.3390/jcm10030403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/22/2022] Open
Abstract
Tumour tissue as a source for molecular profiling and for in vivo models has limitations (e.g., difficult access, limited availability, single time point, potential heterogeneity between primary and metastatic sites). Conversely, liquid biopsies provide an easily accessible approach, enabling timely and longitudinal interrogation of the tumour molecular makeup, with increased ability to capture spatial and temporal intra-tumour heterogeneity compared to tumour tissue. Blood-borne biomarker assays (e.g., circulating tumour cells (CTCs), circulating free/tumour DNA (cf/ctDNA)) pose unique opportunities for aiding in the molecular characterisation and phenotypic subtyping of neuroendocrine neoplasms and will be discussed in this article.
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Affiliation(s)
- Dinakshi Shah
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester M20 4BX, UK; (D.S.); (A.L.)
| | - Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester M20 4BX, UK; (D.S.); (A.L.)
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK;
| | - Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester M20 4BX, UK; (D.S.); (A.L.)
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK;
| | - Mairéad G McNamara
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester M20 4BX, UK; (D.S.); (A.L.)
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK;
- Correspondence:
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