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Feng Y, Yu L, Xu Q, Wei Z, Gan Z, Nie X, Xiao Y. Bioreaction-Compatible Bivariate Lanthanide MOF Sensor Enables Stimulus-Multiresponsive Platform for ctDNA On-Site Detection. Anal Chem 2024; 96:10953-10961. [PMID: 38922180 DOI: 10.1021/acs.analchem.4c01207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Detection of circulating tumor DNA (ctDNA) in liquid biopsy is of great importance for tumor diagnosis but difficult due to its low amount in bodily fluids. Herein, a novel ctDNA detection platform is established by quantifying DNA amplification by-product pyrophosphate (PPi) using a newly designed bivariable lanthanide metal-organic framework (Ln-MOF), namely, Ce/Eu-DPA MOF (CE-24, DPA = pyridine-2,6-dicarboxylic acid). CE-24 MOF exhibits ultrafast dual-response (fluorescence enhancement and enzyme-activity inhibition) to PPi stimuli by virtue of host-guest interaction. The platform is applied to detecting colon carcinoma-related ctDNA (KARS G12D mutation) combined with the isothermal nucleic acid exponential amplification reaction (EXPAR). ctDNA triggers the generation of a large amount of PPi, and the ctDNA quantification is achieved through the ratio fluorescence/colorimetric dual-mode assay of PPi. The combination of the EXPAR and the dual-mode PPi sensing allows the ctDNA assay method to be low-cost, convenient, bioreaction-compatible (freedom from the interference of bioreaction systems), sensitive (limit of detection down to 101 fM), and suitable for on-site detection. To the best of our knowledge, this work is the first application of Ln-MOF for ctDNA detection, and it provides a novel universal strategy for the rapid detection of nucleic acid biomarkers in point-of-care scenarios.
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Affiliation(s)
- Yumin Feng
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Long Yu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qi Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhongyu Wei
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhiwen Gan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xilin Nie
- Yujin Bio-pharma Wuhan CNBG Co. LTD., Wuhan 430207, China
| | - Yuxiu Xiao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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2
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Sementsov M, Ott L, Kött J, Sartori A, Lusque A, Degenhardt S, Segier B, Heidrich I, Volkmer B, Greinert R, Mohr P, Simon R, Stadler JC, Irwin D, Koch C, Andreas A, Deitert B, Thewes V, Trumpp A, Schneeweiss A, Belloum Y, Peine S, Wikman H, Riethdorf S, Schneider SW, Gebhardt C, Pantel K, Keller L. Mutation analysis in individual circulating tumor cells depicts intratumor heterogeneity in melanoma. EMBO Mol Med 2024; 16:1560-1578. [PMID: 38898234 PMCID: PMC11250829 DOI: 10.1038/s44321-024-00082-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating tumor DNA (ctDNA) is the cornerstone of liquid biopsy diagnostics, revealing clinically relevant genomic aberrations from blood of cancer patients. Genomic analysis of single circulating tumor cells (CTCs) could provide additional insights into intra-patient heterogeneity, but it requires whole-genome amplification (WGA) of DNA, which might introduce bias. Here, we describe a novel approach based on mass spectrometry for mutation detection from individual CTCs not requiring WGA and complex bioinformatics pipelines. After establishment of our protocol on tumor cell line-derived single cells, it was validated on CTCs of 33 metastatic melanoma patients and the mutations were compared to those obtained from tumor tissue and ctDNA. Although concordance with tumor tissue was superior for ctDNA over CTC analysis, a larger number of mutations were found within CTCs compared to ctDNA (p = 0.039), including mutations in melanoma driver genes, or those associated with resistance to therapy or metastasis. Thus, our results demonstrate proof-of-principle data that CTC analysis can provide clinically relevant genomic information that is not redundant to tumor tissue or ctDNA analysis.
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Affiliation(s)
- Mark Sementsov
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Ott
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Kött
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Amelie Lusque
- Biostatistics & Health Data Science Unit, Institut Claudius-Regaud, IUCT-Oncopole, Toulouse, France
| | - Sarah Degenhardt
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Bertille Segier
- Biostatistics & Health Data Science Unit, Institut Claudius-Regaud, IUCT-Oncopole, Toulouse, France
| | - Isabel Heidrich
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Beate Volkmer
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Rüdiger Greinert
- Department of Molecular Cell Biology, Skin Cancer Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Peter Mohr
- Department of Dermatology, Elbe Kliniken Buxtehude, 21614, Buxtehude, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia-Christina Stadler
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Claudia Koch
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antje Andreas
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Deitert
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Verena Thewes
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harriett Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan W Schneider
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoffer Gebhardt
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Laura Keller
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- CRCT, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.
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Scaini MC, Catoni C, Poggiana C, Pigozzo J, Piccin L, Leone K, Scarabello I, Facchinetti A, Menin C, Elefanti L, Pellegrini S, Aleotti V, Vidotto R, Schiavi F, Fabozzi A, Chiarion-Sileni V, Rosato A. A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance. NPJ Precis Oncol 2024; 8:78. [PMID: 38548846 PMCID: PMC10978909 DOI: 10.1038/s41698-024-00567-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Melanoma heterogeneity is a hurdle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcomes, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker for the real-time tracing of disease evolution. Thus, we aimed to correlate liquid biopsy dynamics with treatment response and progression by devising a multiplatform approach applied to longitudinal melanoma patient monitoring. We conceived an approach that exploits Next Generation Sequencing (NGS) and droplet digital PCR, as well as the FDA-cleared platform CellSearch, to analyze circulating tumor DNA (ctDNA) trend and circulating melanoma cell (CMC) count, together with their customized genetic and copy number variation analysis. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, followed for up to 28 months. BRAF mutations were detected in the plasma of 82% of patients. Single nucleotide variants known or suspected to confer resistance were identified in 70% of patients. Moreover, the amount of ctDNA, both at baseline and during response, correlated with the type and duration of the response itself, and the CMC count was confirmed to be a prognostic biomarker. This work provides proof of principle of the power of this approach and paves the way for a validation study aimed at evaluating early ctDNA-guided treatment decisions in stage IV melanoma. The NGS-based molecular profile complemented the analysis of ctDNA trend and, together with CMC analysis, revealed to be useful in capturing tumor evolution.
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Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Jacopo Pigozzo
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Luisa Piccin
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Kevin Leone
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Ilaria Scarabello
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Stefania Pellegrini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Riccardo Vidotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Francesca Schiavi
- Familial Cancer Clinic, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Oncology Unit 3, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | | | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
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Warburton L, Reid A, Amanuel B, Calapre L, Millward M, Gray E. Detectable ctDNA at the time of treatment cessation of ipilimumab and nivolumab for toxicity predicts disease progression in advanced melanoma patients. Front Oncol 2023; 13:1280730. [PMID: 38179171 PMCID: PMC10766351 DOI: 10.3389/fonc.2023.1280730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Background Immune checkpoint inhibition (ICI) has led to unprecedented outcomes for melanoma patients but is associated with toxicity. ICI resumption after high grade irAEs poses a significant challenge in the clinical management of melanoma patients and there are no biomarkers that can help identify patients that might benefit from resuming treatment. This study aims to determine if circulating tumor DNA (ctDNA) levels at the time of treatment-limiting irAE could guide treatment decisions in this clinical context. Methods This is a retrospective exploratory biomarker study from 34 patients treated with combination ICI for stage IV melanoma. Patients had a treatment-limiting toxicity and a baseline plasma collection prior to commencing ICI and within 6 weeks of stopping therapy. Blood samples were tested for ctDNA at baseline and cessation therapy. Results Median progression free survival (PFS) and overall survival (OS) have not been reached (24-month PFS rate 54% and OS rate 72.3%). PD occurred in 47% (16/34) of patients. Median PFS with detectable ctDNA from plasma collected at the time of toxicity was 6.5 months while not reached (NR) with undetectable levels (HR: 4.0, 95% CI 0.95-17.5, p=0.0023). Median OS with detectable ctDNA at cessation for toxicity was 19.4 months and NR for undetectable ctDNA (HR: 3.9, 95%CI 20.8-18.6, p=0.024). Positive ctDNA at the time of cessation was highly specific (specificity 0.94, 95% CI 0.74-0.99, PPV 0.88, 95% CI 0.53-0.99). However, ctDNA negativity has low sensitivity as a predictor of ongoing disease control (sensitivity 0.437, 95% CI 0.23-0.67). Notably, 4/9 (44%) ctDNA negative patients who had disease progression had brain only disease progression. Conclusions Undetectable ctDNA and CR on imaging after stopping immunotherapy for toxicity results in high rates of long-term durable control. For patients with immunotherapy related toxicity, who have persistent ctDNA at 8 - 12 weeks, the risk of disease progression is significant.
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Affiliation(s)
- Lydia Warburton
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Anna Reid
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Benhur Amanuel
- Anatomical Pathology, PathWest, Queen Elizabeth II (QEII) Medical Centre, Nedlands, WA, Australia
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia
| | - Leslie Calapre
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Michael Millward
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Elin Gray
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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5
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Beasley AB, de Bruyn DP, Calapre L, Al-Ogaili Z, Isaacs TW, Bentel J, Reid AL, Dwarkasing RS, Pereira MR, Khattak MA, Meniawy TM, Millward M, Brosens E, de Klein A, Chen FK, Kiliҫ E, Gray ES. Detection of metastases using circulating tumour DNA in uveal melanoma. J Cancer Res Clin Oncol 2023; 149:14953-14963. [PMID: 37608028 PMCID: PMC10602949 DOI: 10.1007/s00432-023-05271-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Approximately 50% of uveal melanoma (UM) patients will develop metastatic disease depending on the genetic features of the primary tumour. Patients need 3-12 monthly scans, depending on their prognosis, which is costly and often non-specific. Circulating tumour DNA (ctDNA) quantification could serve as a test to detect and monitor patients for early signs of metastasis and therapeutic response. METHODS We assessed ctDNA as a biomarker in three distinct UM cohorts using droplet-digital PCR: (A) a retrospective analysis of primary UM patients to predict metastases; (B) a prospective analysis of UM patients after resolution of their primary tumour for early detection of metastases; and (C) monitoring treatment response in metastatic UM patients. RESULTS Cohort A: ctDNA levels were not associated with the development of metastases. Cohort B: ctDNA was detected in 17/25 (68%) with radiological diagnosis of metastases. ctDNA was the strongest predictor of overall survival in a multivariate analysis (HR = 15.8, 95% CI 1.7-151.2, p = 0.017). Cohort C: ctDNA monitoring of patients undergoing immunotherapy revealed a reduction in the levels of ctDNA in patients with combination immunotherapy. CONCLUSIONS Our proof-of-concept study shows the biomarker feasibility potential of ctDNA monitoring in for the clinical management of uveal melanoma patients.
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Affiliation(s)
- Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
| | - Daniël P de Bruyn
- Department of Ophthalmology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Zeyad Al-Ogaili
- Department of Molecular Imaging and Therapy Service, Fiona Stanley Hospital, Murdoch, WA, 6150, Australia
| | - Timothy W Isaacs
- Perth Retina, Subiaco, WA, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Crawley, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
| | - Jacqueline Bentel
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Anna L Reid
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Roy S Dwarkasing
- Department of Radiology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
| | - Michelle R Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Muhammad A Khattak
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, WA, Australia
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Tarek M Meniawy
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Michael Millward
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Crawley, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Emine Kiliҫ
- Department of Ophthalmology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
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Tébar-Martínez R, Martín-Arana J, Gimeno-Valiente F, Tarazona N, Rentero-Garrido P, Cervantes A. Strategies for improving detection of circulating tumor DNA using next generation sequencing. Cancer Treat Rev 2023; 119:102595. [PMID: 37390697 DOI: 10.1016/j.ctrv.2023.102595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.
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Affiliation(s)
- Roberto Tébar-Martínez
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Jorge Martín-Arana
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Bioinformatics Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College of London Cancer Institute, 72 Huntley St, WC1E 6DD London, United Kingdom.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
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7
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Calapre L, Giardina T, Beasley AB, Reid AL, Stewart C, Amanuel B, Meniawy TM, Gray ES. Identification of TP53 mutations in circulating tumour DNA in high grade serous ovarian carcinoma using next generation sequencing technologies. Sci Rep 2023; 13:278. [PMID: 36609632 PMCID: PMC9822997 DOI: 10.1038/s41598-023-27445-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
Plasma circulating tumour DNA (ctDNA) has been suggested to be a viable biomarker of response to treatment in patients with high grade serous ovarian carcinoma (HGSOC). TP53 mutations are present in more than 90% of HGSOCs but somatic variants are distributed across all exonic regions of the gene, requiring next generation sequencing (NGS) technologies for mutational analysis. In this study, we compared the suitability of the Accel (Swift) and Oncomine (ThermoFisher) panels for identification of TP53 mutations in ctDNA of HGSOC patients (N = 10). Only 6 patients (60%) were found to have TP53 mutations using the ACCEL panel but the addition of molecular tags in the Oncomine panel improved ctDNA detection with at least one mutation detected in all cases (100%). Orthogonal validation of the 14 somatic variants found by Oncomine, using droplet digital PCR, confirmed 79% (11/14) of the identified mutations. Overall, the Oncomine panel with unique molecular identifiers (UMI) appears more useful for ctDNA analysis in HGSOC.
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Affiliation(s)
- Leslie Calapre
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia
| | - Tindaro Giardina
- grid.415461.30000 0004 6091 201XAnatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA Australia
| | - Aaron B. Beasley
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia ,grid.1038.a0000 0004 0389 4302Centre for Precision Health, Edith Cowan University, Joondalup, WA Australia
| | - Anna L. Reid
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia ,grid.1038.a0000 0004 0389 4302Centre for Precision Health, Edith Cowan University, Joondalup, WA Australia
| | - Colin Stewart
- grid.415461.30000 0004 6091 201XAnatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA Australia ,grid.1012.20000 0004 1936 7910Medical School, University of Western Australia, Crawley, WA Australia
| | - Benhur Amanuel
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia ,grid.415461.30000 0004 6091 201XAnatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA Australia ,grid.1012.20000 0004 1936 7910Medical School, University of Western Australia, Crawley, WA Australia
| | - Tarek M. Meniawy
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia ,grid.1012.20000 0004 1936 7910Medical School, University of Western Australia, Crawley, WA Australia ,grid.3521.50000 0004 0437 5942Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA Australia
| | - Elin S. Gray
- grid.1038.a0000 0004 0389 4302School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA Australia ,grid.415461.30000 0004 6091 201XAnatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA Australia
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8
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Catoni C, Poggiana C, Facchinetti A, Pigozzo J, Piccin L, Chiarion-Sileni V, Rosato A, Minervini G, Scaini MC. Investigating the Retained Inhibitory Effect of Cobimetinib against p.P124L Mutated MEK1: A Combined Liquid Biopsy and in Silico Approach. Cancers (Basel) 2022; 14:cancers14174153. [PMID: 36077693 PMCID: PMC9454486 DOI: 10.3390/cancers14174153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The systemic treatment of metastatic melanoma has radically changed, due to an improvement in the understanding of its genetic landscape and the advent of targeted therapy. However, the response to BRAF/MEK inhibitors is transitory, and big efforts were made to identify the mechanisms underlying the resistance. We exploited a combined approach, encompassing liquid biopsy analysis and molecular dynamics simulation, for tracking tumor evolution, and in parallel defining the best treatment option. The samples at different time points were collected from a BRAF-mutant melanoma patient who developed an early resistance to dabrafenib/trametinib. The analysis of the circulating tumor DNA (ctDNA) identified the MEK1 p.P124L mutation that confers resistance to trametinib. With an in silico modeling, we identified cobimetinib as an alternative MEK inhibitor, and consequently suggested a therapy switch to vemurafenib/cobimetinib. The patient response was followed by ctDNA tracking and circulating melanoma cell (CMC) count. The cobimetinib administration led to an important reduction in the BRAF p.V600E and MEK1 p.P124L allele fractions and in the CMC number, features suggestive of a putative response. In summary, this study emphasizes the usefulness of a liquid biopsy-based approach combined with in silico simulation, to track real-time tumor evolution while assessing the best treatment option.
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Affiliation(s)
- Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Jacopo Pigozzo
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Luisa Piccin
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Vanna Chiarion-Sileni
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
- Correspondence: (A.R.); (M.C.S.)
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, 35121 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Correspondence: (A.R.); (M.C.S.)
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9
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Corvigno S, Johnson AM, Wong KK, Cho MS, Afshar-Kharghan V, Menter DG, Sood AK. Novel Markers for Liquid Biopsies in Cancer Management: Circulating Platelets and Extracellular Vesicles. Mol Cancer Ther 2022; 21:1067-1075. [PMID: 35545008 DOI: 10.1158/1535-7163.mct-22-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023]
Abstract
Although radiologic imaging and histologic assessment of tumor tissues are classic approaches for diagnosis and monitoring of treatment response, they have many limitations. These include challenges in distinguishing benign from malignant masses, difficult access to the tumor, high cost of the procedures, and tumor heterogeneity. In this setting, liquid biopsy has emerged as a potential alternative for both diagnostic and monitoring purposes. The approaches to liquid biopsy include cell-free DNA/circulating tumor DNA, long and micro noncoding RNAs, proteins/peptides, carbohydrates/lectins, lipids, and metabolites. Other approaches include detection and analysis of circulating tumor cells, extracellular vesicles, and tumor-activated platelets. Ultimately, reliable use of liquid biopsies requires bioinformatics and statistical integration of multiple datasets to achieve approval in a Clinical Laboratory Improvement Amendments setting. This review provides a balanced and critical assessment of recent discoveries regarding tumor-derived biomarkers in liquid biopsies along with the potential and pitfalls for cancer detection and longitudinal monitoring.
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Affiliation(s)
- Sara Corvigno
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anna Maria Johnson
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kwong-Kwok Wong
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Min Soon Cho
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vahid Afshar-Kharghan
- Division of Internal Medicine, Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David G Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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10
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Diefenbach RJ, Lee JH, Stewart A, Menzies AM, Carlino MS, Saw RPM, Stretch JR, Long GV, Scolyer RA, Rizos H. Anchored Multiplex PCR Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Front Oncol 2022; 12:820510. [PMID: 35494035 PMCID: PMC9039342 DOI: 10.3389/fonc.2022.820510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Detection of melanoma mutations using circulating tumor DNA (ctDNA) is a potential alternative to using genomic DNA from invasive tissue biopsies. To date, mutations in the GC-rich TERT promoter region, which is commonly mutated in melanoma, have been technically difficult to detect in ctDNA using next-generation sequencing (NGS) panels. In this study, we developed a custom melanoma NGS panel for detection of ctDNA, which encompasses the top 15 gene mutations in melanoma including the TERT promoter. We analyzed 21 stage III and IV melanoma patient samples who were treatment-naïve or on therapy. The overall detection rate of the custom panel, based on BRAF/NRAS/TERT promoter mutations, was 14/21 (67%) patient samples which included a TERT C250T mutation in one BRAF and NRAS mutation negative sample. A BRAF or NRAS mutation was detected in the ctDNA of 13/21 (62%) patients while TERT promoter mutations were detected in 10/21 (48%) patients. Co-occurrence of TERT promoter mutations with BRAF or NRAS mutations was found in 9/10 (90%) patients. The custom ctDNA panel showed a concordance of 16/21 (76%) with tissue based-detection and included 12 BRAF/NRAS mutation positive and 4 BRAF/NRAS mutation negative patients. The ctDNA mutation detection rate for stage IV was 12/16 (75%) and for stage III was 1/5 (20%). Based on BRAF, NRAS and TERT promoter mutations, the custom melanoma panel displayed a limit of detection of ~0.2% mutant allele frequency and showed significant correlation with droplet digital PCR. For one patient, a novel MAP2K1 H119Y mutation was detected in an NRAS/BRAF/TERT promoter mutation negative background. To increase the detection rate to >90% for stage IV melanoma patients, we plan to expand our custom panel to 50 genes. This study represents one of the first to successfully detect TERT promoter mutations in ctDNA from cutaneous melanoma patients using a targeted NGS panel.
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Affiliation(s)
- Russell J Diefenbach
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Jenny H Lee
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Ashleigh Stewart
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
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11
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Sobczuk P, Kozak K, Kopeć S, Rogala P, Świtaj T, Koseła-Paterczyk H, Gos A, Tysarowski A, Rutkowski P. The Use of ctDNA for BRAF Mutation Testing in Routine Clinical Practice in Patients with Advanced Melanoma. Cancers (Basel) 2022; 14:cancers14030777. [PMID: 35159044 PMCID: PMC8833667 DOI: 10.3390/cancers14030777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/31/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Assessment of BRAF mutation status is mandatory in advanced, previously untreated melanoma patients since it is present in 40–50% of cases and allows treatment with specific inhibitors. The testing is usually performed on the primary tumor or metastatic lesion; however, in some cases, liquid biopsy and analysis of circulating tumor DNA in the blood can be used. The aim of our study was to evaluate the clinical utility of plasma circulating tumor DNA analysis for BRAF mutation. We identified 46 patients (21 female, 25 male) who underwent such a procedure. A BRAF mutation was found in 45.7% of liquid biopsies and 44.8% of tissue samples. In 18 patients, therapy with BRAF/MEK inhibitors was initiated on the basis of the result of liquid biopsy. Our study confirms the clinical utility of BRAF mutation detection in liquid biopsy. Abstract Assessment of BRAF mutation status is mandatory in advanced, treatment-naïve melanoma patients. Liquid biopsy can be an alternative in cases with inadequate or unavailable tumor tissue. The aim of our study was to evaluate the clinical utility of plasma circulating tumor DNA analysis for BRAF mutation testing and to assess outcomes of therapy with BRAF/MEK inhibitors initiated based on the liquid biopsy results. This was a retrospective single-center analysis of 46 patients (21 female, 25 male) with advanced melanoma who underwent circulating tumor DNA (ctDNA) BRAF mutation testing. A BRAF mutation was found in 45.7% (21/46) of liquid biopsies and 44.8% (13/29) of tissue samples. In patients with both ctDNA and tissue samples (n = 29), the concordance between the results of both tests was 82.8%. A BRAF mutation was detected in 7/17 (41.2%) patients with only ctDNA analysis. In 18 patients, therapy with BRAF/MEK inhibitors was initiated on the basis of the result of liquid biopsy. The objective response rate was 77.8 %, and the median PFS was 6.0 months. Our study confirms the clinical utility of BRAF mutation detection in plasma ctDNA. This study provides initial real-world data showing that treatment with BRAF/MEK inhibitors could be commenced based on liquid biopsy results.
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Affiliation(s)
- Paweł Sobczuk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
- Department of Experimental and Clinical Physiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-097 Warsaw, Poland
- Correspondence:
| | - Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
| | - Sylwia Kopeć
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
| | - Paweł Rogala
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
| | - Tomasz Świtaj
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
| | - Hanna Koseła-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
| | - Aleksandra Gos
- Department Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.G.); (A.T.)
| | - Andrzej Tysarowski
- Department Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.G.); (A.T.)
- Cancer Molecular and Genetic Diagnostics Department, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (K.K.); (S.K.); (P.R.); (T.Ś.); (H.K.-P.); (P.R.)
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12
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Detection of clinical progression through plasma ctDNA in metastatic melanoma patients: a comparison to radiological progression. Br J Cancer 2022; 126:401-408. [PMID: 34373567 PMCID: PMC8810871 DOI: 10.1038/s41416-021-01507-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The validity of circulating tumour DNA (ctDNA) as an indicator of disease progression compared to medical imaging in patients with metastatic melanoma requires detailed evaluation. METHODS Here, we carried out a retrospective ctDNA analysis of 108 plasma samples collected at the time of disease progression. We also analysed a validation cohort of 66 metastatic melanoma patients monitored prospectively after response to systemic therapy. RESULTS ctDNA was detected in 62% of patients at the time of disease progression. For 67 patients that responded to treatment, the mean ctDNA level at progressive disease was significantly higher than at the time of response (P < 0.0001). However, only 30 of these 67 (45%) patients had a statistically significant increase in ctDNA by Poisson test. A validation cohort of 66 metastatic melanoma patients monitored prospectively indicated a 56% detection rate of ctDNA at progression, with only two cases showing increased ctDNA prior to radiological progression. Finally, a correlation between ctDNA levels and metabolic tumour burden was only observed in treatment naïve patients but not at the time of progression in a subgroup of patients failing BRAF inhibition (N = 15). CONCLUSIONS These results highlight the low efficacy of ctDNA to detect disease progression in melanoma when compared mainly to standard positron emission tomography imaging.
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13
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Gracie L, Pan Y, Atenafu EG, Ward DG, Teng M, Pallan L, Stevens NM, Khoja L. Circulating tumour DNA (ctDNA) in metastatic melanoma, a systematic review and meta-analysis. Eur J Cancer 2021; 158:191-207. [PMID: 34757258 DOI: 10.1016/j.ejca.2021.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/31/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Circulating tumour DNA (ctDNA) is an emerging biomarker in melanoma. We performed a systematic review and meta-analysis to explore its clinical utility as a prognostic, pharmacodynamic (PD) and predictive biomarker. METHODS A systematic search was conducted from Jan 2015 to April 2021, of the electronic databases PubMed, Cochrane Library and Ovid MEDLINE to identify studies. Studies were restricted to those published in English within the last 5 years, evaluating ctDNA in humans in ≥10 patients. Survival data were extracted for meta-analysis using pooled treatment effect (TE), i.e. log hazard ratios (HRs) and corresponding standard error of TE for progression-free survival or overall survival differences in patients who were ctDNA positive or negative. PRISMA statement guidelines were followed. RESULTS A meta-analysis of 19 studies grouped according to methodology of ctDNA detection, revealed a combined estimate for HR of progression-free survival (13 studies using droplet digital Polymerase Chain Reaction (ddPCR) methodology (N = 1002) of 2.10 (95% CI: 1.71-2.59) revealing a poorer prognosis when ctDNA was detected. This result was confirmed in the smaller analysis of (non-ddPCR, N = 347) five studies: HR = 2.45 (95% CI: 1.29-4.63). Similar findings were found in the overall survival analysis of nine studies (ddPCR methodology, N = 841) where the combined HR was 2.78 (95% CI: 2.21-3.49) and of the five studies (non-ddPCR methodology, N = 326) where the combined HR was 2.58 (95% CI: 1.74-3.84). Serial ctDNA levels on treatment showed a pharmacodynamic role reflecting response or resistance earlier than radiological assessment. CONCLUSIONS Circulating tumour DNA is a predictive, prognostic and PD biomarker in melanoma. Technical standardisation of assays is required before clinical adoption.
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Affiliation(s)
- Lara Gracie
- College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yi Pan
- Centre for Computational Biology and Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eshetu G Atenafu
- Biostatistics Department, Princess Margaret Cancer Center, University Health Network, University Way, Toronto, Ontario, Canada
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mabel Teng
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Department of Oncology, Birmingham B15 2TH, UK
| | - Lallit Pallan
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Department of Oncology, Birmingham B15 2TH, UK
| | - Neil M Stevens
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Leila Khoja
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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14
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Berger M, Thueringer A, Franz D, Dandachi N, Talakić E, Richtig G, Richtig E, Rohrer PM, Koch L, Wolf IH, Koch C, Rainer BM, Koeller M, Pichler M, Gerritsmann H, Kashofer K, Aigelsreiter A. Circulating Tumor DNA as a Marker for Treatment Response in Metastatic Melanoma Patients Using Next-Generation Sequencing-A Prospective Feasibility Study. Cancers (Basel) 2021; 13:3101. [PMID: 34205831 PMCID: PMC8233754 DOI: 10.3390/cancers13123101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 01/05/2023] Open
Abstract
We prospectively performed a longitudinal analysis of circulating tumor DNA (ctDNA) from 149 plasma samples and CT scans in Stage III and IV metastatic melanoma patients (n = 20) treated with targeted agents or immunotherapy using two custom next-generation sequencing (NGS) Ion AmpliSeq™ HD panels including 60 and 81 amplicons in 18 genes, respectively. Concordance of matching cancer-associated mutations in tissue and plasma was 73.3%. Mutant allele frequency (MAF) levels showed a range from 0.04% to 28.7%, well detectable with NGS technologies utilizing single molecule tagging like the AmpliSeq™ HD workflow. Median followup time of the tissue and/or plasma positive cohort (n = 15) was 24.6 months and median progression-free survival (PFS) was 7.8 months. Higher MAF ≥ 1% at baseline was not significantly associated with a risk of progression (Odds Ratio = 0.15; p = 0.155). Although a trend could be seen, MAF levels did not differ significantly over time between patients with and without a PFS event (p = 0.745). Depending on the cell-free DNA amount, NGS achieved a sensitivity down to 0.1% MAF and allowed for parallel analysis of multiple mutations and previously unknown mutations. Our study indicates that NGS gene panels could be useful for monitoring disease burden during therapy with ctDNA in melanoma patients.
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Affiliation(s)
- Marina Berger
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Andrea Thueringer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (A.T.); (D.F.)
| | - Doritt Franz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (A.T.); (D.F.)
| | - Nadia Dandachi
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria; (N.D.); (G.R.); (M.P.)
| | - Emina Talakić
- Department of Radiology, Medical University of Graz, 8036 Graz, Austria;
| | - Georg Richtig
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria; (N.D.); (G.R.); (M.P.)
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Peter Michael Rohrer
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Lukas Koch
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Ingrid Hildegard Wolf
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Catharina Koch
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Barbara Margaretha Rainer
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria; (M.B.); (E.R.); (P.M.R.); (L.K.); (I.H.W.); (C.K.); (B.M.R.)
| | - Maximilian Koeller
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria; (N.D.); (G.R.); (M.P.)
| | - Hanno Gerritsmann
- Medical Affairs Oncology, Novartis Pharma GmbH, 1020 Vienna, Austria;
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (A.T.); (D.F.)
| | - Ariane Aigelsreiter
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria; (A.T.); (D.F.)
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15
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Naqvi MF, Vo HH, Vining D, Tsimberidou AM. Prolonged response to treatment based on cell-free DNA analysis and molecular profiling in three patients with metastatic cancer: a case series. Ther Adv Med Oncol 2021; 13:17588359211001538. [PMID: 33995588 PMCID: PMC8107674 DOI: 10.1177/17588359211001538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/10/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Patients with advanced and/or metastatic solid tumors have limited treatment options. Mutations that serve as biomarkers of carcinogenesis can be found in cell-free DNA of patients’ plasma. Analysis of circulating tumor DNA (ctDNA) was developed as a non-invasive, cost-effective alternative to tumor biopsy when such biopsy is not technically feasible or it is associated with high risk for complications. The role of ctDNA in precision oncology is promising but its clinical significance across tumor types remains to be validated. We report a case series of three heavily pretreated patients with advanced solid tumors who received matched targeted therapy based on ctDNA analysis and/or tumor molecular profiling. Case presentation: Three patients with advanced, metastatic cancer and the following characteristics are presented: a 71-year-old woman with ovarian cancer and BRCA2 mutation identified in ctDNA and tumor tissue was treated with a PARP inhibitor and achieved partial response by RECIST (Response Evaluation Criteria in Solid Tumors) for 22.6+ months; a 40-year-old woman with adenoid cystic carcinoma of the parotid gland was treated with a MEK/RAF pathway inhibitor on the basis of RAF1 amplification on ctDNA analysis and had stable disease for 20.2 months; and a 56-year-old woman with breast cancer and a BRCA1 mutation identified by ctDNA analysis was treated with a PARP inhibitor and achieved stable disease for 9.1 months. All three patients are alive at the time of this report. Conclusions: These results suggest that ctDNA analysis can contribute to selection of targeted therapy in patients with advanced, metastatic cancer. Prospective clinical trials to evaluate and optimize ctDNA biomarkers, as well as the integration of novel and/or alternative targeted therapies, are warranted to fully assess the role of ctDNA analysis in cancer therapy. Trial registration: www.clinicaltrials.gov (NCT02152254). Registered May 28, 2014. https://www.clinicaltrials.gov/ct2/show/NCT02152254. MD Anderson protocol # PA12-1161 (approval ID IRB1 FWA00000121) and # PA11-0377 (approval ID IRB4 FWA00005015).
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Affiliation(s)
- Mohammad Faraz Naqvi
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry Hiep Vo
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Vining
- Department of Abdominal Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Apostolia-Maria Tsimberidou
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Unit 455, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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16
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Powter B, Jeffreys SA, Sareen H, Cooper A, Brungs D, Po J, Roberts T, Koh ES, Scott KF, Sajinovic M, Vessey JY, de Souza P, Becker TM. Human TERT promoter mutations as a prognostic biomarker in glioma. J Cancer Res Clin Oncol 2021; 147:1007-1017. [PMID: 33547950 PMCID: PMC7954705 DOI: 10.1007/s00432-021-03536-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/27/2022]
Abstract
The TERT promoter (pTERT) mutations, C228T and C250T, play a significant role in malignant transformation by telomerase activation, oncogenesis and immortalisation of cells. C228T and C250T are emerging as important biomarkers in many cancers including glioblastoma multiforme (GBM), where the prevalence of these mutations is as high as 80%. Additionally, the rs2853669 single nucleotide polymorphism (SNP) may cooperate with these pTERT mutations in modulating progression and overall survival in GBM. Using liquid biopsies, pTERT mutations, C228T and C250T, and other clinically relevant biomarkers can be easily detected with high precision and sensitivity, facilitating longitudinal analysis throughout therapy and aid in cancer patient management. In this review, we explore the potential for pTERT mutation analysis, via liquid biopsy, for its potential use in personalised cancer therapy. We evaluate the relationship between pTERT mutations and other biomarkers as well as their potential clinical utility in early detection, prognostication, monitoring of cancer progress, with the main focus being on brain cancer.
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Affiliation(s)
- Branka Powter
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.
| | - Sarah A Jeffreys
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia
| | - Heena Sareen
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,Western Clinical School, University of New South Wales South, Goulburn St, Liverpool, NSW, 2170, Australia
| | - Adam Cooper
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia.,Cancer Therapy Centre, Liverpool Hospital, Elizabeth St and Goulburn St, Liverpool, NSW, 2170, Australia
| | - Daniel Brungs
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Joseph Po
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia
| | - Tara Roberts
- School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia.,Western Clinical School, University of New South Wales South, Goulburn St, Liverpool, NSW, 2170, Australia
| | - Eng-Siew Koh
- Western Clinical School, University of New South Wales South, Goulburn St, Liverpool, NSW, 2170, Australia.,Cancer Therapy Centre, Liverpool Hospital, Elizabeth St and Goulburn St, Liverpool, NSW, 2170, Australia
| | - Kieran F Scott
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia
| | - Mila Sajinovic
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia
| | - Joey Y Vessey
- Cancer Therapy Centre, Liverpool Hospital, Elizabeth St and Goulburn St, Liverpool, NSW, 2170, Australia
| | - Paul de Souza
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia.,Western Clinical School, University of New South Wales South, Goulburn St, Liverpool, NSW, 2170, Australia.,Cancer Therapy Centre, Liverpool Hospital, Elizabeth St and Goulburn St, Liverpool, NSW, 2170, Australia.,School of Medicine, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Therese M Becker
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW, 2170, Australia.,School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia.,Western Clinical School, University of New South Wales South, Goulburn St, Liverpool, NSW, 2170, Australia
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17
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da Costa VR, Bim LV, Pacheco e Silva LDP, Colloza-Gama GA, Bastos AU, Delcelo R, Oler G, Cerutti JM. Advances in Detecting Low Prevalence Somatic TERT Promoter Mutations in Papillary Thyroid Carcinoma. Front Endocrinol (Lausanne) 2021; 12:643151. [PMID: 33776938 PMCID: PMC7994758 DOI: 10.3389/fendo.2021.643151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Two recurrent TERT (telomerase reverse transcriptase) promoter mutations, C228T and C250T, have been reported in thyroid carcinomas and were correlated with high-risk clinicopathological features and a worse prognosis. Although far more frequent in the poorly differentiated and undifferentiated thyroid cancer, the TERT promoter mutations play a significant role on PTC recurrence and disease-specific mortality. However, the prevalence varies considerably through studies and it is uncertain if these differences are due to population variation or the methodology used to detect TERT mutations. In this study we aim to compare three different strategies to detect TERT promoter mutations in PTC. METHODS DNA was isolated from formalin-fixed paraffin-embedded (FFPE) specimens from 89 PTC and 40 paired lymph node metastases. The prevalence of the hot spot TERT C228T and C250T mutations was assessed in FFPE samples using TaqMan SNP genotyping assays. Random samples were tested by Sanger Sequencing and droplet digital PCR (ddPCR). RESULTS In general, 16 out of 89 (18%) PTC samples and 14 out of 40 (35%) lymph node metastases harbored TERT promoter mutations by TaqMan assay. Sanger sequencing, performed in random selected samples, failed to detect TERT mutations in four samples that were positive by TaqMan SNP genotyping assay. Remarkably, ddPCR assay allowed detection of TERT promoter mutations in six samples that harbor very low mutant allele frequency (≤ 2%) and were negative by both genotype assay and Sanger Sequencing. CONCLUSION This study observed a good concordance among the methodologies used to detect TERT promoter mutations when a high percentage of mutated alleles was present. Sanger analysis demonstrated a limit of detection for mutated alleles. Therefore, the prevalence of TERT promoter mutations in PTC may be higher than previously reported, since most studies have conventionally used Sanger sequencing. The efficient characterization of genetic alterations that are used as preoperative or postoperative diagnostic, risk stratification of the patient and individualized treatment decisions, mainly in highly heterogeneous tumors, require highly sensitive and specific approaches.
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Affiliation(s)
- Vitor Rodrigues da Costa
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Larissa Valdemarin Bim
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Gabriel Avelar Colloza-Gama
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - André Uchimura Bastos
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
- Repare DNA Laboratory, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Rosana Delcelo
- Department of Pathology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gisele Oler
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Division of Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Janete Maria Cerutti,
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18
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Marsavela G, Johansson PA, Pereira MR, McEvoy AC, Reid AL, Robinson C, Warburton L, Khattak MA, Meniawy TM, Amanuel B, Millward M, Hayward NK, Ziman MR, Gray ES, Calapre L. The Prognostic Impact of Circulating Tumour DNA in Melanoma Patients Treated with Systemic Therapies-Beyond BRAF Mutant Detection. Cancers (Basel) 2020; 12:E3793. [PMID: 33339135 PMCID: PMC7765660 DOI: 10.3390/cancers12123793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
In this study, we evaluated the predictive value of circulating tumour DNA (ctDNA) to inform therapeutic outcomes in metastatic melanoma patients receiving systemic therapies. We analysed 142 plasma samples from metastatic melanoma patients prior to commencement of systemic therapy: 70 were treated with BRAF/MEK inhibitors and 72 with immunotherapies. Patient-specific droplet digital polymerase chain reaction assays were designed for ctDNA detection. Plasma ctDNA was detected in 56% of patients prior to first-line anti-PD1 and/or anti-CTLA-4 treatment. The detection rate in the immunotherapy cohort was comparably lower than those with BRAF inhibitors (76%, p = 0.0149). Decreasing ctDNA levels within 12 weeks of treatment was strongly concordant with treatment response (Cohen's k = 0.798, p < 0.001) and predictive of longer progression free survival. Notably, a slower kinetic of ctDNA decline was observed in patients treated with immunotherapy compared to those on BRAF/MEK inhibitors. Whole exome sequencing of ctDNA was also conducted in 9 patients commencing anti-PD-1 therapy to derive tumour mutational burden (TMB) and neoepitope load measurements. The results showed a trend of high TMB and neoepitope load in responders compared to non-responders. Overall, our data suggest that changes in ctDNA can serve as an early indicator of outcomes in metastatic melanoma patients treated with systemic therapies and therefore may serve as a tool to guide treatment decisions.
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Affiliation(s)
- Gabriela Marsavela
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
| | - Peter A. Johansson
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia; (P.A.J.); (N.K.H.)
| | - Michelle R. Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
| | - Ashleigh C. McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
| | - Anna L. Reid
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
| | - Cleo Robinson
- Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia;
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Lydia Warburton
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6010, Australia;
| | - Muhammad A. Khattak
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
- School of Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Western Australia 6150, Australia
| | - Tarek M. Meniawy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6010, Australia;
- School of Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Benhur Amanuel
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
- Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia;
- School of Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6010, Australia;
- School of Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicholas K. Hayward
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia; (P.A.J.); (N.K.H.)
| | - Melanie R. Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia 6027, Australia; (G.M.); (M.R.P.); (A.C.M.); (A.L.R.); (L.W.); (M.A.K.); (T.M.M.); (B.A.); (M.R.Z.); (L.C.)
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19
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Circulating Tumour DNA in Advanced Melanoma Patients Ceasing PD1 Inhibition in the Absence of Disease Progression. Cancers (Basel) 2020; 12:cancers12113486. [PMID: 33238616 PMCID: PMC7700409 DOI: 10.3390/cancers12113486] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Immunotherapy is an effective treatment that harnesses the immune system to fight cancer. Drugs such as immune checkpoint inhibitors have demonstrated efficacy in the treatment of advanced melanoma. However, the optimal duration of treatment is not well established. The aim of our retrospective study was to analyse the outcomes of patients who have stopped immunotherapy treatment for advanced melanoma after durable disease control. Furthermore, we assessed circulating tumour DNA (ctDNA), which is shed from the tumour into the bloodstream, to determine its validity as a predictive biomarker of disease progression after treatment was stopped. We demonstrated that stopping treatment after durable disease control results in excellent short- to medium-term prognosis and ctDNA present at the time of stopping treatment is a strong predictor of disease recurrence. Abstract Immunotherapy is an important and established treatment option for patients with advanced melanoma. Initial anti-PD1 trials arbitrarily defined a two-year treatment duration, but a shorter treatment duration may be appropriate. In this study, we retrospectively assessed 70 patients who stopped anti-PD1 therapy in the absence of progressive disease (PD) to determine clinical outcomes. In our cohort, the median time on treatment was 11.8 months. Complete response was attained at time of anti-PD1 discontinuation in 61 (87%). After a median follow up of 34.2 months (range: 2–70.8) post discontinuation, 81% remained disease free. Using ddPCR, we determine the utility of circulating tumour DNA (ctDNA) to predict progressive disease after cessation (n = 38). There was a significant association between presence of ctDNA at cessation and disease progression (p = 0.012, Fisher’s exact test) and this conferred a negative and positive predictive value of 0.82 (95% CI: 0.645–0.930) and 0.80 (95% CI 0.284–0.995), respectively. Additionally, dichotomised treatment-free survival in patients with or without ctDNA at cessation was significantly longer in the latter group (p < 0.001, HR: 0.008, 95% CI: 0.001–0.079). Overall, our study confirms that durable disease control can be achieved with cessation of therapy in the absence of disease progression and undetectable ctDNA at cessation was associated with longer treatment-free survival.
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20
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Warburton L, Meniawy TM, Calapre L, Pereira M, McEvoy A, Ziman M, Gray ES, Millward M. Stopping targeted therapy for complete responders in advanced BRAF mutant melanoma. Sci Rep 2020; 10:18878. [PMID: 33139839 PMCID: PMC7606504 DOI: 10.1038/s41598-020-75837-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
BRAF inhibitors revolutionised the management of melanoma patients and although resistance occurs, there is a subgroup of patients who maintain durable disease control. For those cases with durable complete response (CR) it is not clear whether it is safe to cease therapy. Here we identified 13 patients treated with BRAF +/- MEK inhibitors, who cease therapy after prolonged CR (median = 34 months, range 20-74). Recurrence was observed in 3/13 (23%) patients. In the remaining 10 patients with sustained CR off therapy, the median follow up after discontinuation was 19 months (range 8-36). We retrospectively measured ctDNA levels using droplet digital PCR (ddPCR) in longitudinal plasma samples. CtDNA levels were undetectable in 11/13 cases after cessation and remained undetectable in patients in CR (10/13). CtDNA eventually became detectable in 2/3 cases with disease recurrence, but remained undetectable in 1 patient with brain only progression. Our study suggests that consideration could be given to ceasing targeted therapy in the context of prolonged treatment, durable response and no evidence of residual disease as measured by ctDNA.
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Affiliation(s)
- L Warburton
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - T M Meniawy
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia
| | - L Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - M Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - A McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - M Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia
| | - E S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
| | - M Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia
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21
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Marczynski GT, Laus AC, Dos Reis MB, Reis RM, Vazquez VDL. Circulating tumor DNA (ctDNA) detection is associated with shorter progression-free survival in advanced melanoma patients. Sci Rep 2020; 10:18682. [PMID: 33122747 PMCID: PMC7596487 DOI: 10.1038/s41598-020-75792-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
BRAF, NRAS and TERT mutations occur in more than 2/3 of melanomas. Its detection in patient's blood, as circulating tumor DNA (ctDNA), represents a possibility for identification and monitoring of metastatic disease. We proposed to standardize a liquid biopsy platform to identify hotspot mutations in BRAF, NRAS and TERT in plasma samples from advanced melanoma patients and investigate whether it was associated to clinical outcome. Firstly, we performed digital polymerase chain reaction using tumor cell lines for validation and determination of limit of detection (LOD) of each assay and screened plasma samples from healthy individuals to determine the limit of blank (LOB). Then, we selected 19 stage III and IV patients and determined the somatic mutations status in tumor tissue and track them in patients' plasma. We established a specific and sensitive methodology with a LOD ranging from 0.13 to 0.37%, and LOB ranging from of 0 to 5.201 copies/reaction. Somatic mutations occurred in 17/19 (89%) patients, of whom seven (41%) had ctDNA detectable their paired plasma. ctDNA detection was associated with shorter progression free survival (p = 0.01). In conclusion, our data support the use of ctDNA as prognosis biomarker, suggesting that patients with detectable levels have an unfavorable outcome.
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Affiliation(s)
- Gabriella Taques Marczynski
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Mariana Bisarro Dos Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil.
- Surgery Department of Melanoma, Sarcoma and Mesenchymal Tumors, Barretos Cancer Hospital, Barretos, Brazil.
- Barretos School of Health Sciences Dr. Paulo Prata - FACISB, Barretos, Brazil.
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22
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Marsavela G, Lee J, Calapre L, Wong SQ, Pereira MR, McEvoy AC, Reid AL, Robinson C, Warburton L, Abed A, Khattak MA, Meniawy TM, Dawson SJ, Sandhu S, Carlino MS, Menzies AM, Scolyer RA, Long GV, Amanuel B, Millward M, Ziman MR, Rizos H, Gray ES. Circulating Tumor DNA Predicts Outcome from First-, but not Second-line Treatment and Identifies Melanoma Patients Who May Benefit from Combination Immunotherapy. Clin Cancer Res 2020; 26:5926-5933. [PMID: 33067256 DOI: 10.1158/1078-0432.ccr-20-2251] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/29/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE We evaluated the predictive value of pretreatment ctDNA to inform therapeutic outcomes in patients with metastatic melanoma relative to type and line of treatment. EXPERIMENTAL DESIGN Plasma circulating tumor DNA (ctDNA) was quantified in 125 samples collected from 110 patients prior to commencing treatment with immune checkpoint inhibitors (ICIs), as first- (n = 32) or second-line (n = 27) regimens, or prior to commencing first-line BRAF/MEK inhibitor therapy (n = 66). An external validation cohort included 128 patients commencing ICI therapies in the first- (N = 77) or second-line (N = 51) settings. RESULTS In the discovery cohort, low ctDNA (≤20 copies/mL) prior to commencing therapy predicted longer progression-free survival (PFS) in patients treated with first-line ICIs [HR, 0.20; 95% confidence interval (CI) 0.07-0.53; P < 0.0001], but not in the second-line setting. An independent cohort validated that ctDNA is predictive of PFS in the first-line setting (HR, 0.42; 95% CI, 0.22-0.83; P = 0.006), but not in the second-line ICI setting. Moreover, ctDNA prior to commencing ICI treatment was not predictive of PFS for patients pretreated with BRAF/MEK inhibitors in either the discovery or validation cohorts. Reduced PFS and overall survival were observed in patients with high ctDNA receiving anti-PD-1 monotherapy, relative to those treated with combination anti-CTLA-4/anti-PD-1 inhibitors. CONCLUSIONS Pretreatment ctDNA is a reliable indicator of patient outcome in the first-line ICI treatment setting, but not in the second-line ICI setting, especially in patients pretreated with BRAF/MEK inhibitors. Preliminary evidence indicated that treatment-naïve patients with high ctDNA may preferentially benefit from combined ICIs.
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Affiliation(s)
- Gabriela Marsavela
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Jenny Lee
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Michelle R Pereira
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Ashleigh C McEvoy
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Anna L Reid
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Cleo Robinson
- Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Australia.,School of Biomedical Science, University of Western Australia, Crawley, Australia
| | - Lydia Warburton
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Afaf Abed
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Australia
| | - Muhammad A Khattak
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, Australia.,School of Medicine, University of Western Australia, Crawley, Australia
| | - Tarek M Meniawy
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Medicine, University of Western Australia, Crawley, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, New South Wales, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Northern Sydney Cancer Centre, Royal North Shore Hospital, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Medical School, The University of Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Northern Sydney Cancer Centre, Royal North Shore Hospital, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Benhur Amanuel
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Australia.,School of Medicine, University of Western Australia, Crawley, Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Medicine, University of Western Australia, Crawley, Australia
| | - Melanie R Ziman
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.,School of Biomedical Science, University of Western Australia, Crawley, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia.
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23
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Sacco A, Forgione L, Carotenuto M, De Luca A, Ascierto PA, Botti G, Normanno N. Circulating Tumor DNA Testing Opens New Perspectives in Melanoma Management. Cancers (Basel) 2020; 12:E2914. [PMID: 33050536 PMCID: PMC7601606 DOI: 10.3390/cancers12102914] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Malignant melanoma accounts for about 1% of all skin cancers, but it causes most of the skin cancer-related deaths. Circulating tumor DNA (ctDNA) testing is emerging as a relevant tool for the diagnosis and monitoring of cancer. The availability of highly sensitive techniques, including next generation sequencing (NGS)-based panels, has increased the fields of application of ctDNA testing. While ctDNA-based tests for the early detection of melanoma are not available yet, perioperative ctDNA analysis in patients with surgically resectable melanoma offers relevant prognostic information: i) the detection of ctDNA before surgery correlates with the extent and the aggressiveness of the disease; ii) ctDNA testing after surgery/adjuvant therapy identifies minimal residual disease; iii) testing ctDNA during the follow-up can detect a tumor recurrence, anticipating clinical/radiological progression. In patients with advanced melanoma, several studies have demonstrated that the analysis of ctDNA can better depict tumor heterogeneity and provides relevant prognostic information. In addition, ctDNA testing during treatment allows assessing the response to systemic therapy and identifying resistance mechanisms. Although validation in prospective clinical trials is needed for most of these approaches, ctDNA testing opens up new scenarios in the management of melanoma patients that could lead to improvements in the diagnosis and therapy of this disease.
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Affiliation(s)
- Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Laura Forgione
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Marianeve Carotenuto
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Paolo A. Ascierto
- Department of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Napoli, Italy;
| | - Gerardo Botti
- Scientific Direction, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Napoli, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
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24
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Diefenbach RJ, Lee JH, Menzies AM, Carlino MS, Long GV, Saw RPM, Howle JR, Spillane AJ, Scolyer RA, Kefford RF, Rizos H. Design and Testing of a Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Cancers (Basel) 2020; 12:E2228. [PMID: 32785074 PMCID: PMC7465941 DOI: 10.3390/cancers12082228] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Detection of melanoma-associated mutations using circulating tumor DNA (ctDNA) from plasma is a potential alternative to using genomic DNA from invasive tissue biopsies. In this study, we developed a custom melanoma next-generation sequencing (NGS) panel which includes 123 amplicons in 30 genes covering driver and targetable mutations and alterations associated with treatment resistance. Analysis of a cohort of 74 stage III and IV treatment-naïve melanoma patients revealed that sensitivity of ctDNA detection was influenced by the amount of circulating-free DNA (cfDNA) input and stage of melanoma. At the recommended cfDNA input quantity of 20 ng (available in 28/74 patients), at least one cancer-associated mutation was detected in the ctDNA of 84% of stage IV patients and 47% of stage III patients with a limit of detection for mutant allele frequency (MAF) of 0.2%. This custom melanoma panel showed significant correlation with droplet digital PCR (ddPCR) and provided a more comprehensive melanoma mutation profile. Our custom panel could be further optimized by replacing amplicons spanning the TERT promoter, which did not perform well due to the high GC content. To increase the detection rate to 90% of stage IV melanoma and decrease the sensitivity to 0.1% MAF, we recommend increasing the volume of plasma to 8 mL to achieve minimal recommended cfDNA input and the refinement of poorly performing amplicons. Our panel can also be expanded to include new targetable and treatment resistance mutations to improve the tracking of treatment response and resistance in melanoma patients treated with systemic drug therapies.
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Affiliation(s)
- Russell J. Diefenbach
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Jenny H. Lee
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Alexander M. Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Matteo S. Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Julie R. Howle
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Breast and Melanoma Surgery Department, Division of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, NSW 2050, Australia
| | - Richard F. Kefford
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
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25
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Diefenbach RJ, Lee JH, Rizos H. Methylated circulating tumor DNA as a biomarker in cutaneous melanoma. Melanoma Manag 2020; 7:MMT46. [PMID: 32922728 PMCID: PMC7475794 DOI: 10.2217/mmt-2020-0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Russell J Diefenbach
- Department of Biomedical Sciences, Faculty of Medicine, Health & Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia
| | - Jenny H Lee
- Department of Biomedical Sciences, Faculty of Medicine, Health & Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health & Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia
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26
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Pedersen JG, Madsen AT, Gammelgaard KR, Aggerholm-Pedersen N, Sørensen BS, Øllegaard TH, Jakobsen MR. Inflammatory Cytokines and ctDNA Are Biomarkers for Progression in Advanced-Stage Melanoma Patients Receiving Checkpoint Inhibitors. Cancers (Basel) 2020; 12:E1414. [PMID: 32486146 PMCID: PMC7353055 DOI: 10.3390/cancers12061414] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Checkpoint inhibitors have significantly improved treatment of metastatic melanoma. However, 40-60% of patients do not respond to therapy, emphasizing the need for better predictive biomarkers for treatment response to immune checkpoint inhibitors. Prorammed death-ligand 1(PD-L1) expression in tumor cells is currently used as a predictive biomarker; however, it lacks specificity. Therefore, it is of utmost importance to identify other novel biomarkers that can predict treatment outcome. EXPERIMENTAL DESIGN We studied a small cohort of 16 patients with advanced-stage melanoma treated with first-line checkpoint inhibitors. Plasma samples were collected prior to treatment initiation and continuously during the first year of treatment. Circulating tumor DNA (ctDNA) level and the expression of ten inflammatory cytokines were analyzed. RESULTS We found that the ctDNA-level in a blood sample collected after 6-8 weeks of therapy is predictive for response to checkpoint inhibitors. Patients with undetectable ctDNA had significantly longer progression-free survival (PFS) compared with patients with detectable ctDNA (median 26.3 vs. 2.1 months, p = 0.006). In parallel, we identified that high levels of the cytokines monocyte chemoattractant protein 1 (MCP1) and tumor necrosis factor a(TNFa) in baseline blood samples were significantly associated with longer PFS compared to low level of these cytokines (median not reached vs. 8.2 months p = 0.0008). CONCLUSIONS These findings suggest that the levels of ctDNA, MCP1, and TNFa in baseline and early follow-up samples can predict disease progression in metastatic melanoma patients treated with checkpoint inhibitors. Potentially, these minimally invasive biomarkers may identify responders from non-responders.
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Affiliation(s)
- Jesper Geert Pedersen
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus, Denmark; (J.G.P.); (K.R.G.)
| | - Anne Tranberg Madsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8000 Aarhus, Denmark; (A.T.M.); (B.S.S.)
| | - Kristine Raaby Gammelgaard
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus, Denmark; (J.G.P.); (K.R.G.)
| | | | - Boe Sandahl Sørensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8000 Aarhus, Denmark; (A.T.M.); (B.S.S.)
| | | | - Martin Roelsgaard Jakobsen
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus, Denmark; (J.G.P.); (K.R.G.)
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27
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Trung NT, Hoan NX, Trung PQ, Binh MT, Van Tong H, Toan NL, Bang MH, Song LH. Clinical significance of combined circulating TERT promoter mutations and miR-122 expression for screening HBV-related hepatocellular carcinoma. Sci Rep 2020; 10:8181. [PMID: 32424223 PMCID: PMC7234991 DOI: 10.1038/s41598-020-65213-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
Telomerase reverse-transcriptase (TERT) gene promoter mutations in circulating cell-free DNA (cfDNA) as well as the levels of circulating microRNA-122 (miR-122) have been reported as potential noninvasive biomarkers for several. This study evaluates the diagnostic performance of potent biomarker-based panels composing of serological AFP, miR-122 and circulating TERT promoter mutations for screening HBV-related HCC. TERT promoter mutations (C228T and C250T) and miR-122 expression were assessed in the plasma samples from 249 patients with HBV-related liver diseases by nested PCR and qRT-PCR assays, respectively. The diagnostic values of TERT promoter mutations, miR-122 expression and biomarker-based panels were assessed by computation of the area under the curve (AUC). Nested-PCR assays were optimized to detect C228T and C250T mutations in TERT promoter with detection limit of 1%. The common hotspot C228T was observed in 22 HCC cases. The triple combinatory panel (AFP@TERT@miR-122) acquired the best diagnostic value to distinguish HCC from CHB (AUC = 0.98), LC (AUC = 0.88) or non-HCC (LC + CHB, AUC = 0.94) compared to the performance of double combinations or single biomarkers, respectively. Notably, among patients with AFP levels≤20 ng/μl, the double combination panel (TERT@miR-122) retains satisfactory diagnostic performance in discriminating HCC from the others (HCC vs. CHB, AUC = 0.96; HCC vs. LC, AUC = 0.88, HCC vs. non-HCC, AUC = 0.94). The triple combination panel AFP@TERT@miR-122 shows a better diagnostic performance for screening HCC in HBV patients, regardless of AFP levels. The newly established panels can be a potential application in clinical practice in Vietnamese setting.
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Affiliation(s)
- Ngo Tat Trung
- Centre for Genetic Consultation and Cancer Screening, 108 Military Central Hospital, Hanoi, Vietnam. .,Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam.
| | - Nghiem Xuan Hoan
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam.,Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam
| | - Pham Quang Trung
- Centre for Genetic Consultation and Cancer Screening, 108 Military Central Hospital, Hanoi, Vietnam.,Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
| | - Mai Thanh Binh
- Department of Gastroenterology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Hoang Van Tong
- Institute of Biomedicine and Pharmacy, Vietnam Military Medical University, Hanoi, Vietnam.,Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Nguyen Linh Toan
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Mai Hong Bang
- Department of Gastroenterology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam. .,Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam.
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28
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Aya-Bonilla CA, Morici M, Hong X, McEvoy AC, Sullivan RJ, Freeman J, Calapre L, Khattak MA, Meniawy T, Millward M, Ziman M, Gray ES. Detection and prognostic role of heterogeneous populations of melanoma circulating tumour cells. Br J Cancer 2020; 122:1059-1067. [PMID: 32037400 PMCID: PMC7109152 DOI: 10.1038/s41416-020-0750-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Circulating tumour cells (CTCs) can be assessed through a minimally invasive blood sample with potential utility as a predictive, prognostic and pharmacodynamic biomarker. The large heterogeneity of melanoma CTCs has hindered their detection and clinical application. METHODS Here we compared two microfluidic devices for the recovery of circulating melanoma cells. The presence of CTCs in 43 blood samples from patients with metastatic melanoma was evaluated using a combination of immunocytochemistry and transcript analyses of five genes by RT-PCR and 19 genes by droplet digital PCR (ddPCR), whereby a CTC score was calculated. Circulating tumour DNA (ctDNA) from the same patient blood sample, was assessed by ddPCR targeting tumour-specific mutations. RESULTS Our analysis revealed an extraordinary heterogeneity amongst melanoma CTCs, with multiple non-overlapping subpopulations. CTC detection using our multimarker approach was associated with shorter overall and progression-free survival. Finally, we found that CTC scores correlated with plasma ctDNA concentrations and had similar pharmacodynamic changes upon treatment initiation. CONCLUSIONS Despite the high phenotypic and molecular heterogeneity of melanoma CTCs, multimarker derived CTC scores could serve as viable tools for prognostication and treatment response monitoring in patients with metastatic melanoma.
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Affiliation(s)
| | - Michael Morici
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Xin Hong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | | | - Ryan Joseph Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - James Freeman
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Muhammad Adnan Khattak
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, WA, Australia
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Tarek Meniawy
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Michael Millward
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Mel Ziman
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
- School of Biomedical Science, University of Western Australia, Crawley, WA, Australia
| | - Elin Solomonovna Gray
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia.
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29
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Detection of Gene Mutations in Liquid Biopsy of Melanoma Patients: Overview and Future Perspectives. Curr Treat Options Oncol 2020; 21:19. [PMID: 32048063 DOI: 10.1007/s11864-020-0708-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OPINION STATEMENT Liquid biopsies are still far from widely implanted in the clinical arena. Issues related to the added sensitivity of this test beyond conventional methods have not been fully resolved. Additionally, issues related to the specificity of these results especially as many cancers may share common mutation need further investigations. One way to resolve this may include the development and testing of large gene panels to add higher specificity. On the other hand, further studies are needed to support the idea that ctDNA or circulating tumor cells may constitute a better representation of the tumor subpopulation that is capable of metastasizing, which will strongly support its clinical value. Finally, survival studies showing a positive impact of this technology will also justify its widespread implementation in clinical practice.
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Palmieri G. Circulating driver gene mutations: what is the impact on melanoma patients' management? Ann Oncol 2019; 30:669-671. [PMID: 30887019 DOI: 10.1093/annonc/mdz090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- G Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy.
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31
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Ice RJ, Chen M, Sidorov M, Le Ho T, Woo RWL, Rodriguez-Brotons A, Luu T, Jian D, Kim KB, Leong SP, Kim H, Kim A, Stone D, Nazarian A, Oh A, Tranah GJ, Nosrati M, de Semir D, Dar AA, Chang S, Desprez PY, Kashani-Sabet M, Soroceanu L, McAllister SD. Drug responses are conserved across patient-derived xenograft models of melanoma leading to identification of novel drug combination therapies. Br J Cancer 2019; 122:648-657. [PMID: 31857724 PMCID: PMC7054294 DOI: 10.1038/s41416-019-0696-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Patient-derived xenograft (PDX) mouse tumour models can predict response to therapy in patients. Predictions made from PDX cultures (PDXC) would allow for more rapid and comprehensive evaluation of potential treatment options for patients, including drug combinations. METHODS We developed a PDX library of BRAF-mutant metastatic melanoma, and a high-throughput drug-screening (HTDS) platform utilising clinically relevant drug exposures. We then evaluated 34 antitumor agents across eight melanoma PDXCs, compared drug response to BRAF and MEK inhibitors alone or in combination with PDXC and the corresponding PDX, and investigated novel drug combinations targeting BRAF inhibitor-resistant melanoma. RESULTS The concordance of cancer-driving mutations across patient, matched PDX and subsequent PDX generations increases as variant allele frequency (VAF) increases. There was a high correlation in the magnitude of response to BRAF and MEK inhibitors between PDXCs and corresponding PDXs. PDXCs and corresponding PDXs from metastatic melanoma patients that progressed on standard-of-care therapy demonstrated similar resistance patterns to BRAF and MEK inhibitor therapy. Importantly, HTDS identified novel drug combinations to target BRAF-resistant melanoma. CONCLUSIONS The biological consistency observed between PDXCs and PDXs suggests that PDXCs may allow for a rapid and comprehensive identification of treatments for aggressive cancers, including combination therapies.
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Affiliation(s)
- Ryan J Ice
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Michelle Chen
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Max Sidorov
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Tam Le Ho
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Rinette W L Woo
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | | | - Tri Luu
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Damon Jian
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Stanley P Leong
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - HanKyul Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Angela Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Des Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Ari Nazarian
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Alyssia Oh
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Mehdi Nosrati
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - David de Semir
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Altaf A Dar
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Stephen Chang
- University of California at San Francisco, School of Pharmacy, Department of Clinical Pharmacy, San Francisco, CA, 94143, USA
| | - Pierre-Yves Desprez
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | | | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Sean D McAllister
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA.
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32
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Jahangiri L, Hurst T. Assessing the Concordance of Genomic Alterations between Circulating-Free DNA and Tumour Tissue in Cancer Patients. Cancers (Basel) 2019; 11:cancers11121938. [PMID: 31817150 PMCID: PMC6966532 DOI: 10.3390/cancers11121938] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Somatic alterations to the genomes of solid tumours, which in some cases represent actionable drivers, provide diagnostic and prognostic insight into these complex diseases. Spatial and longitudinal tracking of somatic genomic alterations (SGAs) in patient tumours has emerged as a new avenue of investigation, not only as a disease monitoring strategy, but also to improve our understanding of heterogeneity and clonal evolution from diagnosis through disease progression. Furthermore, analysis of circulating-free DNA (cfDNA) in the so-called "liquid biopsy" has emerged as a non-invasive method to identify genomic information to inform targeted therapy and may also capture the heterogeneity of the primary and metastatic tumours. Considering the potential of cfDNA analysis as a translational laboratory tool in clinical practice, establishing the extent to which cfDNA represents the SGAs of tumours, particularly actionable driver alterations, becomes a matter of importance, warranting standardisation of methods and practices. Here, we assess the utilisation of cfDNA for molecular profiling of SGAs in tumour tissue across a broad range of solid tumours. Moreover, we examine the underlying factors contributing to discordance of detected SGAs between cfDNA and tumour tissue.
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Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Lab blocks level 3, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Correspondence:
| | - Tara Hurst
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
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33
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Diefenbach RJ, Lee JH, Strbenac D, Yang JYH, Menzies AM, Carlino MS, Long GV, Spillane AJ, Stretch JR, Saw RPM, Thompson JF, Ch’ng S, Scolyer RA, Kefford RF, Rizos H. Analysis of the Whole-Exome Sequencing of Tumor and Circulating Tumor DNA in Metastatic Melanoma. Cancers (Basel) 2019; 11:cancers11121905. [PMID: 31795494 PMCID: PMC6966626 DOI: 10.3390/cancers11121905] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
The use of circulating tumor DNA (ctDNA) to monitor cancer progression and response to therapy has significant potential but there is only limited data on whether this technique can detect the presence of low frequency subclones that may ultimately confer therapy resistance. In this study, we sought to evaluate whether whole-exome sequencing (WES) of ctDNA could accurately profile the mutation landscape of metastatic melanoma. We used WES to identify variants in matched, tumor-derived genomic DNA (gDNA) and plasma-derived ctDNA isolated from a cohort of 10 metastatic cutaneous melanoma patients. WES parameters such as sequencing coverage and total sequencing reads were comparable between gDNA and ctDNA. The mutant allele frequency of common single nucleotide variants was lower in ctDNA, reflecting the lower read depth and minor fraction of ctDNA within the total circulating free DNA pool. There was also variable concordance between gDNA and ctDNA based on the total number and identity of detected variants and this was independent of the tumor biopsy site. Nevertheless, established melanoma driver mutations and several other melanoma-associated mutations were concordant between matched gDNA and ctDNA. This study highlights that WES of ctDNA could capture clinically relevant mutations present in melanoma metastases and that enhanced sequencing sensitivity will be required to identify low frequency mutations.
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Affiliation(s)
- Russell J. Diefenbach
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
| | - Jenny H. Lee
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia; (D.S.); (J.Y.H.Y.)
| | - Jean Y. H. Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia; (D.S.); (J.Y.H.Y.)
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alexander M. Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Matteo S. Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Jonathan R. Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Sydney Ch’ng
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Richard F. Kefford
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (A.J.S.); (J.R.S.); (R.P.M.S.); (J.F.T.); (S.C.); (R.A.S.); (R.F.K.)
- Correspondence: ; Tel.: +61-298-502-762
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Forthun RB, Hovland R, Schuster C, Puntervoll H, Brodal HP, Namløs HM, Aasheim LB, Meza-Zepeda LA, Gjertsen BT, Knappskog S, Straume O. ctDNA detected by ddPCR reveals changes in tumour load in metastatic malignant melanoma treated with bevacizumab. Sci Rep 2019; 9:17471. [PMID: 31767937 PMCID: PMC6877652 DOI: 10.1038/s41598-019-53917-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/05/2019] [Indexed: 12/26/2022] Open
Abstract
Bevacizumab is included in an increasing number of clinical trials. To find biomarkers to predict and monitor treatment response, cancer and angiogenesis relevant mutations in tumour and circulating tumour DNA (ctDNA) were investigated in 26 metastatic melanoma patients treated with bevacizumab. Patients with >1% BRAF/NRAS ctDNA at treatment start had significantly decreased progression free survival (PFS) and overall survival (OS) (PFS: p = 0.019, median 54 vs 774 days, OS: p = 0.026, median 209 vs 1064 days). Patients with >1% BRAF/NRAS ctDNA during treatment showed similar results (PFS: p = 0.002, OS: p = 0.003). ≤1% BRAF/NRAS ctDNA and normal lactate dehydrogenase (LDH) levels both significantly predicted increased response to treatment, but BRAF/NRAS ctDNA was better at predicting response compared to LDH at treatment start (OR 16.94, p = 0.032 vs OR 4.57, p = 0.190), and at predicting PFS (HR 6.76, p = 0.002) and OS (HR 6.78, p = 0.002) during therapy. ctDNA BRAF p.V600D/E/K and NRAS p.G12V/p.Q61K/L/R were better biomarkers for response prediction than TERT promoter mutations (OR 1.50, p = 0.657). Next generation sequencing showed that all patients with ≥2 mutations in angiogenesis-relevant genes had progressive disease, but did not reveal other biomarkers identifying responders. To conclude, ctDNA and LDH are useful biomarkers for both monitoring and predicting response to bevacizumab.
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Affiliation(s)
- Rakel Brendsdal Forthun
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Biosciences, University of Bergen, Bergen, Norway
| | - Cornelia Schuster
- Centre of Cancer Biomarkers, CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hanne Puntervoll
- Centre of Cancer Biomarkers, CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hans Petter Brodal
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Heidi Maria Namløs
- Department of Tumour Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Lars Birger Aasheim
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Department of Tumour Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Norwegian Cancer Genomics Consortium, Institute for Cancer Research, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | - Bjørn Tore Gjertsen
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
- Centre of Cancer Biomarkers, CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stian Knappskog
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Oddbjørn Straume
- Centre of Cancer Biomarkers, CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Oncology, Haukeland University Hospital, Bergen, Norway.
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Calapre L, Warburton L, Millward M, Gray ES. Circulating tumour DNA (ctDNA) as a biomarker in metachronous melanoma and colorectal cancer- a case report. BMC Cancer 2019; 19:1109. [PMID: 31727009 PMCID: PMC6857141 DOI: 10.1186/s12885-019-6336-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/05/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) has emerged as a promising blood-based biomarker for monitoring disease status of patients with advanced cancers. The presence of ctDNA in the blood is a result of biological processes, namely tumour cell apoptosis and/or necrosis, and can be used to monitor different cancers by targeting cancer-specific mutation. CASE PRESENTATION We present the case of a 67 year old Caucasian male that was initially treated with BRAF inhibitors followed by anti-CTLA4 and then anti-PD1 immunotherapy for metastatic melanoma but later developed colorectal cancer. The kinetics of ctDNA derived from each cancer type were monitored targeting BRAF V600R (melanoma) and KRAS G13D (colon cancer), specifically reflected the status of the patient's tumours. In fact, the discordant pattern of BRAF and KRAS ctDNA was significantly correlated with the clinical response of melanoma to pembrolizumab treatment and progression of colorectal cancer noted by PET and/or CT scan. Based on these results, ctDNA can be used to specifically clarify disease status of patients with metachronous cancers. CONCLUSIONS Using cancer-specific mutational targets, we report here for the first time the efficacy of ctDNA to accurately provide a comprehensive outlook of the tumour status of two different cancers within one patient. Thus, ctDNA analysis has a potential clinical utility to delineate clinical information in patients with multiple cancer types.
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Affiliation(s)
- Leslie Calapre
- School of Medical Science, Edith Cowan University, Joondalup, WA Australia
| | - Lydia Warburton
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia Australia
| | - Elin S. Gray
- School of Biomedical Science, University of Western Australia, Crawley, WA Australia
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Zusman E, Sidorov M, Ayala A, Chang J, Singer E, Chen M, Desprez PY, McAllister S, Salomonis N, Chetal K, Prasad G, Kang T, Mark J, Dickinson L, Soroceanu L. Tissues Harvested Using an Automated Surgical Approach Confirm Molecular Heterogeneity of Glioblastoma and Enhance Specimen's Translational Research Value. Front Oncol 2019; 9:1119. [PMID: 31750239 PMCID: PMC6843001 DOI: 10.3389/fonc.2019.01119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Designing effective individualized therapies for GBM requires quality fresh tissue specimens, and a comprehensive molecular profile of this highly heterogenous neoplasm. Novel neuro-surgical approaches, such as the automated resection NICO Myriad™ system, are increasingly used by neurosurgeons to better reach the invasive front of tumors. However, no information exists on how harvesting GBM tissue using this approach may impact the translational research value of the sample. Here, we set out to characterize matched specimens from 15 patients, where one tissue sample was obtained using traditional tumor de-bulking (herein referred to as “en bloc” sample), and the other sample was obtained using the MyriadTM System (herein referred to as “Myriad” sample). We investigated the fidelity of patient derived xenografts (PDXs) for each sample type to the corresponding human tissues and evaluated the added value of sequencing both samples for each patient. Matched en bloc and Myriad samples processed in parallel, were subjected to the following assays: cell viability, self-renewal, in vivo tumorigenicity using an orthotopic model of glioma, genomic sequencing, and pharmacological testing using PI3K-MTOR pathway inhibitors. Our results demonstrate that primary GBM cultures derived from matched specimens grew at similar rates (correlation coefficient R = 0.72), generated equivalent number of neurospheres, and had equivalent tumorigenic potential in vivo (mouse survival correlation coefficient R = 0.93). DNA Sequencing using the Illumina tumor panel amplicons revealed over 70% concordance in non-synonymous mutations between matched human GBM specimens. PDX genomic profiles were also highly concordant with the corresponding patient tissues (>70%). RNA sequencing of paired GBM samples revealed unique genomic variants and differential gene expression between the en bloc and Myriad specimens, with the former molecularly resembling the “tumor core” and the latter resembling the “invasive tumor front” signature. Functionally, we show that primary-derived GBM cells—obtained after fresh specimen's dissociation—are more effectively growth-inhibited by co-targeting non-overlapping mutations enriched in each sample type, suggesting that profiling both specimens more adequately capture the molecular heterogeneity of GBM and may enhance the design accuracy and efficacy of individualized therapies.
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Affiliation(s)
- Edie Zusman
- NorthBay Medical Center, Fairfield, CA, United States
| | - Maxim Sidorov
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
| | - Alexandria Ayala
- Pacific Brain and Spine Medical Group, Eden Medical Center-Sutter Research, Castro Valley, CA, United States
| | - Jimmin Chang
- Pacific Brain and Spine Medical Group, Eden Medical Center-Sutter Research, Castro Valley, CA, United States
| | - Eric Singer
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
| | - Michelle Chen
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
| | - Pierre-Yves Desprez
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
| | - Sean McAllister
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
| | - Nathan Salomonis
- Cincinnati Children's Hospital Medical Center (CCHMC) Biomedical Informatics, Cincinnati, OH, United States
| | - Kashish Chetal
- Cincinnati Children's Hospital Medical Center (CCHMC) Biomedical Informatics, Cincinnati, OH, United States
| | - Gautam Prasad
- Pacific Brain and Spine Medical Group, Eden Medical Center-Sutter Research, Castro Valley, CA, United States
| | - Tyler Kang
- Pacific Brain and Spine Medical Group, Eden Medical Center-Sutter Research, Castro Valley, CA, United States
| | - Joseph Mark
- NICO Corporation, Indianapolis, IN, United States
| | - Lawrence Dickinson
- Pacific Brain and Spine Medical Group, Eden Medical Center-Sutter Research, Castro Valley, CA, United States
| | - Liliana Soroceanu
- California Pacific Medical Center (CPMC) Research Institute, San Francisco, CA, United States
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Asante DB, Calapre L, Ziman M, Meniawy TM, Gray ES. Liquid biopsy in ovarian cancer using circulating tumor DNA and cells: Ready for prime time? Cancer Lett 2019; 468:59-71. [PMID: 31610267 DOI: 10.1016/j.canlet.2019.10.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/06/2019] [Indexed: 01/06/2023]
Abstract
Liquid biopsies hold the potential to inform cancer patient prognosis and to guide treatment decisions at the time when direct tumor biopsy may be impractical due to its invasive nature, inaccessibility and associated complications. Specifically, circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) have shown promising results as companion diagnostic biomarkers for screening, prognostication and/or patient surveillance in many cancer types. In ovarian cancer (OC), CTC and ctDNA analysis allow comprehensive molecular profiling of the primary, metastatic and recurrent tumors. These biomarkers also correlate with overall tumor burden and thus, they provide minimally-invasive means for patient monitoring during clinical course to ascertain therapy response and timely treatment modification in the context of disease relapse. Here, we review recent reports of the potential clinical value of CTC and ctDNA in OC, expatiating on their use in diagnosis and prognosis. We critically appraise the current evidence, and discuss the issues that still need to be addressed before liquid biopsies can be implemented in routine clinical practice for OC management.
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Affiliation(s)
- Du-Bois Asante
- School of Medical and Health Sciences, Edith Cowan University, Australia
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Australia
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, Australia; School of Biomedical Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Tarek M Meniawy
- School of Medical and Health Sciences, Edith Cowan University, Australia; School of Medicine, University of Western Australia, Crawley, Western Australia, Australia; Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Australia.
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Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel. J Mol Diagn 2019; 21:418-426. [PMID: 30731208 DOI: 10.1016/j.jmoldx.2018.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/16/2018] [Accepted: 12/04/2018] [Indexed: 11/20/2022] Open
Abstract
The analysis of circulating tumor DNA provides a minimally invasive molecular interrogation that has the potential to guide treatment selection and disease monitoring. Here, the authors evaluated a custom UltraSEEK melanoma panel for the MassARRAY system, probing for 61 mutations over 13 genes. The analytical sensitivity and clinical accuracy of the UltraSEEK melanoma panel was compared with droplet digital PCR. The blinded analysis of 68 mutations detected in 48 plasma samples from stage IV melanoma patients revealed a concordance of 88% between the two platforms. Further comparison of both methods for the detection of BRAF V600E mutations in 77 plasma samples demonstrated a Cohen's κ of 0.826 (bias-corrected and accelerated 95% CI, 0.669-0.946). These results indicate that the UltraSEEK melanoma panel is as sensitive as droplet digital PCR for the detection of circulating tumor DNA in this cohort of patients but highlight the need for detected variants to be confirmed orthogonally to mitigate any false-positive results. The MassARRAY system enables rapid and sensitive genotyping for the detection of multiple melanoma-associated mutations in plasma.
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