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Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples

The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5′/3′-end expression imbalances is potentially capable of detecting the entire spe...

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Autores principales: Romanko, Aleksandr A., Mulkidjan, Rimma S., Tiurin, Vladislav I., Saitova, Evgeniya S., Preobrazhenskaya, Elena V., Krivosheyeva, Elena A., Mitiushkina, Natalia V., Shestakova, Anna D., Belogubova, Evgeniya V., Ivantsov, Alexandr O., Iyevleva, Aglaya G., Imyanitov, Evgeny N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531831/
https://www.ncbi.nlm.nih.gov/pubmed/37762506
http://dx.doi.org/10.3390/ijms241814203
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author Romanko, Aleksandr A.
Mulkidjan, Rimma S.
Tiurin, Vladislav I.
Saitova, Evgeniya S.
Preobrazhenskaya, Elena V.
Krivosheyeva, Elena A.
Mitiushkina, Natalia V.
Shestakova, Anna D.
Belogubova, Evgeniya V.
Ivantsov, Alexandr O.
Iyevleva, Aglaya G.
Imyanitov, Evgeny N.
author_facet Romanko, Aleksandr A.
Mulkidjan, Rimma S.
Tiurin, Vladislav I.
Saitova, Evgeniya S.
Preobrazhenskaya, Elena V.
Krivosheyeva, Elena A.
Mitiushkina, Natalia V.
Shestakova, Anna D.
Belogubova, Evgeniya V.
Ivantsov, Alexandr O.
Iyevleva, Aglaya G.
Imyanitov, Evgeny N.
author_sort Romanko, Aleksandr A.
collection PubMed
description The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5′/3′-end expression imbalances is potentially capable of detecting the entire spectrum of NTRK gene fusions. Archival tumor specimens obtained from 8075 patients were subjected to manual dissection of tumor cells, DNA/RNA isolation, and cDNA synthesis. The 5′/3′-end expression imbalances in NTRK genes were analyzed by real-time PCR. Further identification of gene rearrangements was performed by variant-specific PCR for 44 common NTRK fusions, and, whenever necessary, by RNA-based next-generation sequencing (NGS). cDNA of sufficient quality was obtained in 7424/8075 (91.9%) tumors. NTRK rearrangements were detected in 7/6436 (0.1%) lung carcinomas, 11/137 (8.0%) pediatric tumors, and 13/851 (1.5%) adult non-lung malignancies. The highest incidence of NTRK translocations was observed in pediatric sarcomas (7/39, 17.9%). Increased frequency of NTRK fusions was seen in microsatellite-unstable colorectal tumors (6/48, 12.5%), salivary gland carcinomas (5/93, 5.4%), and sarcomas (7/143, 4.9%). None of the 1293 lung carcinomas with driver alterations in EGFR/ALK/ROS1/RET/MET oncogenes had NTRK 5′/3′-end expression imbalances. Variant-specific PCR was performed for 744 tumors with a normal 5′/3′-end expression ratio: there were no rearrangements in 172 EGFR/ALK/ROS1/RET/MET-negative lung cancers and 125 pediatric tumors, while NTRK3 fusions were detected in 2/447 (0.5%) non-lung adult malignancies. In conclusion, this study describes a diagnostic pipeline that can be used as a cost-efficient alternative to conventional methods of NTRK1–3 analysis.
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spelling pubmed-105318312023-09-28 Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples Romanko, Aleksandr A. Mulkidjan, Rimma S. Tiurin, Vladislav I. Saitova, Evgeniya S. Preobrazhenskaya, Elena V. Krivosheyeva, Elena A. Mitiushkina, Natalia V. Shestakova, Anna D. Belogubova, Evgeniya V. Ivantsov, Alexandr O. Iyevleva, Aglaya G. Imyanitov, Evgeny N. Int J Mol Sci Communication The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5′/3′-end expression imbalances is potentially capable of detecting the entire spectrum of NTRK gene fusions. Archival tumor specimens obtained from 8075 patients were subjected to manual dissection of tumor cells, DNA/RNA isolation, and cDNA synthesis. The 5′/3′-end expression imbalances in NTRK genes were analyzed by real-time PCR. Further identification of gene rearrangements was performed by variant-specific PCR for 44 common NTRK fusions, and, whenever necessary, by RNA-based next-generation sequencing (NGS). cDNA of sufficient quality was obtained in 7424/8075 (91.9%) tumors. NTRK rearrangements were detected in 7/6436 (0.1%) lung carcinomas, 11/137 (8.0%) pediatric tumors, and 13/851 (1.5%) adult non-lung malignancies. The highest incidence of NTRK translocations was observed in pediatric sarcomas (7/39, 17.9%). Increased frequency of NTRK fusions was seen in microsatellite-unstable colorectal tumors (6/48, 12.5%), salivary gland carcinomas (5/93, 5.4%), and sarcomas (7/143, 4.9%). None of the 1293 lung carcinomas with driver alterations in EGFR/ALK/ROS1/RET/MET oncogenes had NTRK 5′/3′-end expression imbalances. Variant-specific PCR was performed for 744 tumors with a normal 5′/3′-end expression ratio: there were no rearrangements in 172 EGFR/ALK/ROS1/RET/MET-negative lung cancers and 125 pediatric tumors, while NTRK3 fusions were detected in 2/447 (0.5%) non-lung adult malignancies. In conclusion, this study describes a diagnostic pipeline that can be used as a cost-efficient alternative to conventional methods of NTRK1–3 analysis. MDPI 2023-09-17 /pmc/articles/PMC10531831/ /pubmed/37762506 http://dx.doi.org/10.3390/ijms241814203 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Romanko, Aleksandr A.
Mulkidjan, Rimma S.
Tiurin, Vladislav I.
Saitova, Evgeniya S.
Preobrazhenskaya, Elena V.
Krivosheyeva, Elena A.
Mitiushkina, Natalia V.
Shestakova, Anna D.
Belogubova, Evgeniya V.
Ivantsov, Alexandr O.
Iyevleva, Aglaya G.
Imyanitov, Evgeny N.
Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title_full Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title_fullStr Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title_full_unstemmed Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title_short Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples
title_sort cost-efficient detection of ntrk1/2/3 gene fusions: single-center analysis of 8075 tumor samples
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531831/
https://www.ncbi.nlm.nih.gov/pubmed/37762506
http://dx.doi.org/10.3390/ijms241814203
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