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
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)...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-09-01
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| Series: | Molecular Oncology |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/1878-0261.13468 |
| _version_ | 1797690645237727232 |
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| author | Ana Giménez‐Capitán Estela Sánchez‐Herrero Lucía Robado de Lope Andrés Aguilar‐Hernández Ivana Sullivan Virginia Calvo Irene Moya‐Horno Santiago Viteri Carlos Cabrera Cristina Aguado Noelia Armiger Joselyn Valarezo Clara Mayo‐de‐las‐Casas Noemí Reguart Rafael Rosell Mariano Provencio Atocha Romero Miguel A. Molina‐Vila |
| author_facet | Ana Giménez‐Capitán Estela Sánchez‐Herrero Lucía Robado de Lope Andrés Aguilar‐Hernández Ivana Sullivan Virginia Calvo Irene Moya‐Horno Santiago Viteri Carlos Cabrera Cristina Aguado Noelia Armiger Joselyn Valarezo Clara Mayo‐de‐las‐Casas Noemí Reguart Rafael Rosell Mariano Provencio Atocha Romero Miguel A. Molina‐Vila |
| author_sort | Ana Giménez‐Capitán |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T02:02:18Z |
| format | Article |
| id | doaj.art-895f32ea609d4f95922800c025292cd9 |
| institution | Directory Open Access Journal |
| issn | 1574-7891 1878-0261 |
| language | English |
| last_indexed | 2024-03-12T02:02:18Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Molecular Oncology |
| spelling | doaj.art-895f32ea609d4f95922800c025292cd92023-09-07T10:57:03ZengWileyMolecular Oncology1574-78911878-02612023-09-011791884189710.1002/1878-0261.13468Detecting ALK, ROS1, and RET fusions and the METΔex14 splicing variant in liquid biopsies of non‐small‐cell lung cancer patients using RNA‐based techniquesAna Giménez‐Capitán0Estela Sánchez‐Herrero1Lucía Robado de Lope2Andrés Aguilar‐Hernández3Ivana Sullivan4Virginia Calvo5Irene Moya‐Horno6Santiago Viteri7Carlos Cabrera8Cristina Aguado9Noelia Armiger10Joselyn Valarezo11Clara Mayo‐de‐las‐Casas12Noemí Reguart13Rafael Rosell14Mariano Provencio15Atocha Romero16Miguel A. Molina‐Vila17Pangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainAtrys Health Barcelona SpainLiquid Biopsy Laboratory Biomedical Sciences Research Institute Puerta de Hierro‐Majadahonda Madrid SpainDr Rosell Oncology Institute Quirón Dexeus University Hospital Barcelona SpainDr Rosell Oncology Institute Quirón Dexeus University Hospital Barcelona SpainMedical Oncology Department Hospital Universitario Puerta de Hierro‐Majadahonda SpainHospital Universitario General de Cataluña Grupo Quirón Sant Cugat del Vallés SpainUOMI Cancer Center Clínica Mi Tres Torres Barcelona SpainUOMI Cancer Center Clínica Mi Tres Torres Barcelona SpainPangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainPangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainPangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainPangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainHospital Clínic de Barcelona SpainDr Rosell Oncology Institute Quirón Dexeus University Hospital Barcelona SpainMedical Oncology Department Hospital Universitario Puerta de Hierro‐Majadahonda SpainLiquid Biopsy Laboratory Biomedical Sciences Research Institute Puerta de Hierro‐Majadahonda Madrid SpainPangaea Oncology, Laboratory of Oncology Dexeus University Hospital Barcelona SpainALK, 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.https://doi.org/10.1002/1878-0261.13468digital PCRgene fusionsliquid biopsylung cancernCounter assaysplicing variants |
| spellingShingle | Ana Giménez‐Capitán Estela Sánchez‐Herrero Lucía Robado de Lope Andrés Aguilar‐Hernández Ivana Sullivan Virginia Calvo Irene Moya‐Horno Santiago Viteri Carlos Cabrera Cristina Aguado Noelia Armiger Joselyn Valarezo Clara Mayo‐de‐las‐Casas Noemí Reguart Rafael Rosell Mariano Provencio Atocha Romero Miguel A. Molina‐Vila 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 Molecular Oncology digital PCR gene fusions liquid biopsy lung cancer nCounter assay splicing variants |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | digital PCR gene fusions liquid biopsy lung cancer nCounter assay splicing variants |
| url | https://doi.org/10.1002/1878-0261.13468 |
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