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Daems E, Bassini S, Mariën L, Op de Beeck H, Stratulat A, Zwaenepoel K, Vandamme T, Op de Beeck K, Koljenović S, Peeters M, Van Camp G, De Wael K. Singlet oxygen-based photoelectrochemical detection of single-point mutations in the KRAS oncogene. Biosens Bioelectron 2024; 249:115957. [PMID: 38199080 DOI: 10.1016/j.bios.2023.115957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Single nucleotide point mutations in the KRAS oncogene occur frequently in human cancers, rendering them intriguing targets for diagnosis, early detection and personalized treatment. Current detection methods are based on polymerase chain reaction, sometimes combined with next-generation sequencing, which can be expensive, complex and have limited availability. Here, we propose a novel singlet oxygen (1O2)-based photoelectrochemical detection methodology for single-point mutations, using KRAS mutations as a case study. This detection method combines the use of a sandwich assay, magnetic beads and robust chemical photosensitizers, that need only air and light to produce 1O2, to ensure high specificity and sensitivity. We demonstrate that hybridization of the sandwich hybrid at high temperatures enables discrimination between mutated and wild-type sequences with a detection rate of up to 93.9%. Additionally, the presence of background DNA sequences derived from human cell-line DNA, not containing the mutation of interest, did not result in a signal, highlighting the specificity of the methodology. A limit of detection as low as 112 pM (1.25 ng/mL) was achieved without employing any amplification techniques. The developed 1O2-based photoelectrochemical methodology exhibits unique features, including rapidity, ease of use, and affordability, highlighting its immense potential in the field of nucleic acid-based diagnostics.
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Affiliation(s)
- Elise Daems
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium; NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
| | - Simone Bassini
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium; NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
| | - Laura Mariën
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, 2650, Belgium; Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium
| | - Hannah Op de Beeck
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium; NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
| | - Alexandr Stratulat
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium; NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium; Department of Pathology, Antwerp University Hospital, Edegem, 2650, Belgium
| | - Timon Vandamme
- Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium; Department of Oncology and Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, 2650, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, 2650, Belgium; Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium
| | - Senada Koljenović
- Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium; Department of Pathology, Antwerp University Hospital, Edegem, 2650, Belgium
| | - Marc Peeters
- Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium; Department of Oncology and Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital, Edegem, 2650, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, 2650, Belgium; Center for Oncological Research, Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, 2610, Belgium
| | - Karolien De Wael
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium; NANOlab Center of Excellence, University of Antwerp, Antwerp, 2020, Belgium.
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Mariën L, Islam O, Chhajlani S, Lybaert W, Peeters M, Van Camp G, Op de Beeck K, Vandamme T. The Quest for Circulating Biomarkers in Neuroendocrine Neoplasms: a Clinical Perspective. Curr Treat Options Oncol 2023; 24:1833-1851. [PMID: 37989978 DOI: 10.1007/s11864-023-01147-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
OPINION STATEMENT Given the considerable heterogeneity in neuroendocrine neoplasms (NENs), it appears unlikely that a sole biomarker exists capable of fully capturing all useful clinical aspects of these tumors. This is reflected in the abundant number of biomarkers presently available for the diagnosis, prognosis, and monitoring of NEN patients. Although assessment of immunohistochemical and radiological markers remains paramount and often obligatory, there has been a notable surge of interest in circulating biomarkers over the years given the numerous benefits associated with liquid biopsies. Currently, the clinic primarily relies on single-analyte assays such as the chromogranin A assay, but these are far from ideal because of limitations such as compromised sensitivity and specificity as well as a lack of standardization. Consequently, the quest for NEN biomarkers continued with the exploration of multianalyte markers, exemplified by the development of the NETest and ctDNA-based analysis. Here, an extensive panel of markers is simultaneously evaluated to identify distinct signatures that could enhance the accuracy of patient diagnosis, prognosis determination, and response to therapy prediction and monitoring. Given the promising results, the development and implementation of these multianalyte markers are expected to usher in a new era of NEN biomarkers in the clinic. In this review, we will outline both clinically implemented and more experimental circulating markers to provide an update on developments in this rapidly evolving field.
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Affiliation(s)
- Laura Mariën
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Integrated Personalized and Precision Oncology Network (IPPON), Center for Oncological Research (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Odeta Islam
- Integrated Personalized and Precision Oncology Network (IPPON), Center for Oncological Research (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
- NETwerk and Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Siddharth Chhajlani
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- NETwerk and Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Willem Lybaert
- NETwerk and Department of Oncology, VITAZ, Lodewijk de Meesterstraat 5, 9100, Sint-Niklaas, Belgium
| | - Marc Peeters
- Integrated Personalized and Precision Oncology Network (IPPON), Center for Oncological Research (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
- NETwerk and Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650, Edegem, Belgium
- Integrated Personalized and Precision Oncology Network (IPPON), Center for Oncological Research (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Timon Vandamme
- Integrated Personalized and Precision Oncology Network (IPPON), Center for Oncological Research (CORE), University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610, Wilrijk, Belgium.
- NETwerk and Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650, Edegem, Belgium.
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Boons G, Vandamme T, Mariën L, Lybaert W, Roeyen G, Rondou T, Papadimitriou K, Janssens K, Op de Beeck B, Simoens M, Demey W, Dero I, Van Camp G, Peeters M, Op de Beeck K. Longitudinal Copy-Number Alteration Analysis in Plasma Cell-Free DNA of Neuroendocrine Neoplasms is a Novel Specific Biomarker for Diagnosis, Prognosis, and Follow-up. Clin Cancer Res 2022; 28:338-349. [PMID: 34759042 PMCID: PMC9401546 DOI: 10.1158/1078-0432.ccr-21-2291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/01/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE As noninvasive biomarkers are an important unmet need for neuroendocrine neoplasms (NEN), biomarker potential of genome-wide molecular profiling of plasma cell-free DNA (cfDNA) was prospectively studied in patients with NEN. EXPERIMENTAL DESIGN Longitudinal plasma samples were collected from patients with well-differentiated, metastatic gastroenteropancreatic and lung NEN. cfDNA was subjected to shallow whole-genome sequencing to detect genome-wide copy-number alterations (CNA) and estimate circulating tumor DNA (ctDNA) fraction, and correlated to clinicopathologic and survival data. To differentiate pancreatic NENs (PNEN) from pancreatic adenocarcinomas (PAAD) using liquid biopsies, a classification model was trained using tissue-based CNAs and validated in cfDNA. RESULTS One hundred and ninety-five cfDNA samples from 43 patients with NEN were compared with healthy control cfDNA (N = 100). Plasma samples from patients with PNEN (N = 21) were used for comparison with publicly available PNEN tissue (N = 98), PAAD tissue (N = 109), and PAAD cfDNA (N = 96). Thirty percent of the NEN cfDNA samples contained ctDNA and 44% of the patients had at least one ctDNA-positive (ctDNA+) sample. CNAs detected in cfDNA were highly specific for NENs and the classification model could distinguish PAAD and PNEN cfDNA samples with a sensitivity, specificity, and AUC of 62%, 86%, and 79%, respectively. ctDNA-positivity was associated with higher World Health Organization (WHO) grade, primary tumor location, and higher chromogranin A and neuron-specific enolase values. Overall survival was significantly worse for ctDNA+ patients and increased ctDNA fractions were associated with poorer progression-free survival. CONCLUSIONS Sequential genome-wide profiling of plasma cfDNA is a novel, noninvasive biomarker with high specificity for diagnosis, prognosis, and follow-up in metastatic NENs.
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Affiliation(s)
- Gitta Boons
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Timon Vandamme
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium.,NETwerk, Antwerp University Hospital, Edegem, Belgium.,Corresponding Author: Timon Vandamme, NETwerk, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Antwerp, Belgium. Phone: 00-323-821-2111; E-mail:
| | - Laura Mariën
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Willem Lybaert
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Medical Oncology, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Geert Roeyen
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Hepatobiliary, Endocrine and Transplantation Surgery, Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - Tim Rondou
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Gastroenterology, AZ Rivierenland, Bornem, Belgium
| | - Konstantinos Papadimitriou
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Katrien Janssens
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Bart Op de Beeck
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Radiology, Antwerp University Hospital, Edegem, Belgium
| | - Marc Simoens
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Gastroenterology, Ziekenhuis Netwerk Antwerpen, Antwerp, Belgium
| | - Wim Demey
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Medical Oncology, AZ Klina, Brasschaat, Belgium.,Department of Oncology, AZ Voorkempen, Malle, Belgium
| | - Isabel Dero
- NETwerk, Antwerp University Hospital, Edegem, Belgium.,Department of Gastroenterology, Gasthuiszusters Antwerpen, Antwerp, Belgium
| | - Guy Van Camp
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,NETwerk, Antwerp University Hospital, Edegem, Belgium
| | - Ken Op de Beeck
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
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