Detecting ALK, ROS1, and RET fusions and the METΔex14 splicing variant in liquid biopsies of non-small-cell lung cancer patients using RNA-based techniques
Giménez-Capitán, Ana (Hospital Dexeus (Barcelona, Catalunya))
Sánchez-Herrero, Estela (Instituto de Investigación Puerta de Hierro (Madrid))
Robado de Lope, Lucía (Instituto de Investigación Puerta de Hierro (Madrid))
Aguilar-Hernández, Andrés (Quirón Hospital Dexeus (Barcelona, Catalunya))
Sullivan, Ivana (Institut d'Investigació Biomèdica Sant Pau)
Calvo, Virginia (Hospital Universitario Puerta de Hierro Majadahonda (Madrid))
Moya-Horno, Irene (Hospital Universitario General de Cataluña Grupo Quirón)
Viteri, Santiago (Clínica Mi Tres Torres)
Cabrera-Galvez, Carlos (Clínica Mi Tres Torres)
Aguado, Cristina (Hospital Dexeus (Barcelona, Catalunya))
Armiger, Noelia (Hospital Dexeus (Barcelona, Catalunya))
Valarezo, Joselyn (Hospital Dexeus (Barcelona, Catalunya))
Mayo-de-las-Casas, Clara (Hospital Dexeus (Barcelona, Catalunya))
Reguart, Noemi (Hospital Clínic i Provincial de Barcelona)
Rosell, Rafael (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol)
Provencio Pulla, M. (Hospital Universitario Puerta de Hierro Majadahonda (Madrid))
Romero, Atocha (Hospital Universitario Puerta de Hierro Majadahonda (Madrid))
Molina-Vila, Miguel Ángel (Hospital Dexeus (Barcelona, Catalunya))
Universitat Autònoma de Barcelona

Date:	2023
Abstract:	ALK, ROS1, and RET fusions and MET∆ex14 variant associate with response to targeted therapies in non-small-cell lung cancer (NSCLC). Technologies for fusion testing in tissue must be adapted to liquid biopsies, which are often the only material available. In this study, circulating-free RNA (cfRNA) and extracellular vesicle RNA (EV-RNA) were purified from liquid biopsies. Fusion and MET∆ex14 transcripts were analyzed by nCounter (Nanostring) and digital PCR (dPCR) using the QuantStudio System (Applied Biosystems). We found that nCounter detected ALK, ROS1, RET, or MET∆ex14 aberrant transcripts in 28/40 cfRNA samples from positive patients and 0/16 of control individuals (70% sensitivity). Regarding dPCR, aberrant transcripts were detected in the cfRNA of 25/40 positive patients. Concordance between the two techniques was 58%. Inferior results were obtained when analyzing EV-RNA, where nCounter often failed due to a low amount of input RNA. Finally, results of dPCR testing in serial liquid biopsies of five patients correlated with response to targeted therapy. We conclude that nCounter can be used for multiplex detection of fusion and MET∆ex14 transcripts in liquid biopsies, showing a performance comparable with next-generation sequencing platforms. dPCR could be employed for disease follow-up in patients with a known alteration. cfRNA should be preferred over EV-RNA for these analyses.
Grants:	Instituto de Salud Carlos III DTS21/00124
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Digital PCR ; Gene fusions ; Liquid biopsy ; Lung cancer ; Ncounter assay ; Splicing variants
Published in:	Molecular oncology, Vol. 17 Núm. 9 (september 2023) , p. 1884-1897, ISSN 1878-0261

DOI: 10.1002/1878-0261.13468
PMID: 37243883

14 p, 1.2 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut d'Investigació en Ciencies de la Salut Germans Trias i Pujol (IGTP)
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Recerca Sant Pau
Articles > Research articles
Articles > Published articles