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Pedraz-Valdunciel C, Giannoukakos S, Giménez-Capitán A, Fortunato D, Filipska M, Bertran-Alamillo J, Bracht JWP, Drozdowskyj A, Valarezo J, Zarovni N, Fernández-Hilario A, Hackenberg M, Aguilar-Hernández A, Molina-Vila MÁ, Rosell R. Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer. Pharmaceutics 2022; 14:2034. [PMID: 36297470 PMCID: PMC9610636 DOI: 10.3390/pharmaceutics14102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. However, standardized and robust protocols need to be developed to boost their potential in the clinical setting. Although nCounter has been used for the analysis of other liquid biopsy substrates and biomarkers, it has never been employed for EV-circRNA analysis of LC patients. METHODS EVs were isolated from early-stage LC patients (n = 36) and controls (n = 30). Different volumes of plasma, together with different number of pre-amplification cycles, were tested to reach the best nCounter outcome. Differential expression analysis of circRNAs was performed, along with the testing of different machine learning (ML) methods for the development of a prognostic signature for LC. RESULTS A combination of 500 μL of plasma input with 10 cycles of pre-amplification was selected for the rest of the study. Eight circRNAs were found upregulated in LC. Further ML analysis selected a 10-circRNA signature able to discriminate LC from controls with AUC ROC of 0.86. CONCLUSIONS This study validates the use of the nCounter platform for multiplexed EV-circRNA expression studies in LC patient samples, allowing the development of prognostic signatures.
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Affiliation(s)
- Carlos Pedraz-Valdunciel
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Department of Biochemistry, Molecular Biology and Biomedicine, Autonomous University of Barcelona, Campus de Bellaterra, 08193 Barcelona, Spain
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Stavros Giannoukakos
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | - Ana Giménez-Capitán
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Martyna Filipska
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- B Cell Biology Group, Hospital del Mar Biomedical Research Park (IMIM), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Jillian W. P. Bracht
- Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, 1105AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105AZ Amsterdam, The Netherlands
| | - Ana Drozdowskyj
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
| | - Joselyn Valarezo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Alberto Fernández-Hilario
- Department of Computer Science and Artificial Intelligence, DaSCI., University of Granada, 18071 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | | | | | - Rafael Rosell
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
- Catalan Institute of Oncology, Campus Can Ruti, 08916 Badalona, Spain
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