Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer
Carlos Pedraz-Valdunciel,
Stavros Giannoukakos,
Ana Giménez-Capitán,
Diogo Fortunato,
Martyna Filipska,
Jordi Bertran-Alamillo,
Jillian W. P. Bracht,
Ana Drozdowskyj,
Joselyn Valarezo,
Natasa Zarovni,
Alberto Fernández-Hilario,
Michael Hackenberg,
Andrés Aguilar-Hernández,
Miguel Ángel Molina-Vila,
Rafael Rosell
Affiliations
Carlos Pedraz-Valdunciel
Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, 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
Diogo Fortunato
Exosomics SpA, 53100 Siena, Italy
Martyna Filipska
Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, 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
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
Natasa Zarovni
Exosomics SpA, 53100 Siena, Italy
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
Andrés Aguilar-Hernández
Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
Miguel Ángel Molina-Vila
Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
Rafael Rosell
Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
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.
