Comprehensive evaluation of the test for 5'-/3'-end mRNA unbalanced expression as a screening tool for ALK and ROS1 fusions in lung cancer.
Anaplastic Lymphoma Kinase
/ genetics
Carcinoma, Non-Small-Cell Lung
/ diagnosis
Early Detection of Cancer
ErbB Receptors
/ genetics
Gene Rearrangement
Humans
Lung Neoplasms
/ diagnosis
Mutation
Oncogene Proteins, Fusion
/ genetics
Protein-Tyrosine Kinases
/ genetics
Proto-Oncogene Proteins
/ genetics
RNA, Messenger
/ genetics
Receptor Protein-Tyrosine Kinases
/ genetics
Translocation, Genetic
lung cancer
molecular diagnosis
qRT-PCR
targeted therapy
Journal
Cancer medicine
ISSN: 2045-7634
Titre abrégé: Cancer Med
Pays: United States
ID NLM: 101595310
Informations de publication
Date de publication:
09 2022
09 2022
Historique:
revised:
02
02
2022
received:
20
10
2021
accepted:
04
03
2022
pubmed:
25
3
2022
medline:
15
9
2022
entrez:
24
3
2022
Statut:
ppublish
Résumé
Despite the progress in the development of next-generation sequencing (NGS), diagnostic PCR assays remain to be utilized in clinical routine due to their simplicity and low cost. Tests for 5'-/3'-end mRNA unbalanced expression can be used for variant-independent detection of translocations, however, many technical aspects of this methodology require additional investigations. Known ALK/ROS1 fusions and 5'-/3'-end unbalanced expression were analyzed in 2009 EGFR mutation-negative non-small cell lung cancer (NSCLC) samples with RT-PCR tests, which were optimized for the use with FFPE-derived RNA. Variant-specific PCR tests for 4 common ALK and 15 common ROS1 translocations detected 115 (5.7%) and 44 (2.2%) rearrangements, respectively. Virtually all samples with common ALK fusions demonstrated some level of 5'/3' mRNA ends unbalanced expression, and 8 additional NSCLCs with rare ALK fusions were further identified by PCR or NGS among 48 cases selected based on ALK expression measurements. Interestingly, NSCLCs with unbalanced 5'-/3'-end ALK expression but without identified ALK translocations had elevated frequency of RAS mutations (21/40, 53%) suggesting the role of RAS activation in the alternative splicing of ALK gene. In contrast to ALK, only a minority of ROS1 translocation-positive cases demonstrated unbalanced gene expression, with both 5'- and 3'-end mRNA expression being elevated in most of the samples with translocations. Surprisingly, high ROS1 expression level was also found to be characteristic for NSCLCs with activating mutations in other tyrosine kinases such as EGFR, ALK, or MET. Comprehensive ALK analysis can be performed by the test for 5'-/3'-end unbalanced expression with minimal risk of missing an ALK rearrangement. In contrast, the use of the test for 5'-/3'-end unbalanced expression for the detection of ROS1 fusions is complicated; hence, the utilization of variant-specific PCR assays for ROS1 testing is preferable.
Sections du résumé
BACKGROUND
Despite the progress in the development of next-generation sequencing (NGS), diagnostic PCR assays remain to be utilized in clinical routine due to their simplicity and low cost. Tests for 5'-/3'-end mRNA unbalanced expression can be used for variant-independent detection of translocations, however, many technical aspects of this methodology require additional investigations.
METHODS
Known ALK/ROS1 fusions and 5'-/3'-end unbalanced expression were analyzed in 2009 EGFR mutation-negative non-small cell lung cancer (NSCLC) samples with RT-PCR tests, which were optimized for the use with FFPE-derived RNA.
RESULTS
Variant-specific PCR tests for 4 common ALK and 15 common ROS1 translocations detected 115 (5.7%) and 44 (2.2%) rearrangements, respectively. Virtually all samples with common ALK fusions demonstrated some level of 5'/3' mRNA ends unbalanced expression, and 8 additional NSCLCs with rare ALK fusions were further identified by PCR or NGS among 48 cases selected based on ALK expression measurements. Interestingly, NSCLCs with unbalanced 5'-/3'-end ALK expression but without identified ALK translocations had elevated frequency of RAS mutations (21/40, 53%) suggesting the role of RAS activation in the alternative splicing of ALK gene. In contrast to ALK, only a minority of ROS1 translocation-positive cases demonstrated unbalanced gene expression, with both 5'- and 3'-end mRNA expression being elevated in most of the samples with translocations. Surprisingly, high ROS1 expression level was also found to be characteristic for NSCLCs with activating mutations in other tyrosine kinases such as EGFR, ALK, or MET.
CONCLUSIONS
Comprehensive ALK analysis can be performed by the test for 5'-/3'-end unbalanced expression with minimal risk of missing an ALK rearrangement. In contrast, the use of the test for 5'-/3'-end unbalanced expression for the detection of ROS1 fusions is complicated; hence, the utilization of variant-specific PCR assays for ROS1 testing is preferable.
Identifiants
pubmed: 35322575
doi: 10.1002/cam4.4686
pmc: PMC9468436
doi:
Substances chimiques
Oncogene Proteins, Fusion
0
Proto-Oncogene Proteins
0
RNA, Messenger
0
Anaplastic Lymphoma Kinase
EC 2.7.10.1
ErbB Receptors
EC 2.7.10.1
Protein-Tyrosine Kinases
EC 2.7.10.1
ROS1 protein, human
EC 2.7.10.1
Receptor Protein-Tyrosine Kinases
EC 2.7.10.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3226-3237Informations de copyright
© 2022 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.
Références
Science. 2015 Jan 23;347(6220):1260419
pubmed: 25613900
Clin Cancer Res. 2013 May 1;19(9):2584-91
pubmed: 23515407
Sci Rep. 2016 Feb 22;6:21418
pubmed: 26898768
PLoS One. 2007 Dec 05;2(12):e1261
pubmed: 18060057
Clin Cancer Res. 2012 Sep 1;18(17):4725-32
pubmed: 22791881
Mol Med Rep. 2018 Aug;18(2):2191-2197
pubmed: 29956783
Int J Mol Sci. 2021 Jan 09;22(2):
pubmed: 33435440
J Exp Clin Cancer Res. 2018 Mar 27;37(1):68
pubmed: 29587818
Exp Mol Pathol. 2009 Oct;87(2):146-51
pubmed: 19619529
Biotechniques. 2006 May;40(5):649-57
pubmed: 16708763
Biotech Histochem. 2018;93(5):373-386
pubmed: 30113239
Crit Rev Oncol Hematol. 2021 Jan;157:103194
pubmed: 33316418
Ann Glob Health. 2019 Jan 22;85(1):
pubmed: 30741509
Biochimie. 2019 Oct;165:267-274
pubmed: 31472177
Oncotarget. 2016 Jun 14;7(24):37160-37176
pubmed: 27206799
J Thorac Oncol. 2014 Mar;9(3):307-15
pubmed: 24495999
J Mol Diagn. 2014 Mar;16(2):229-43
pubmed: 24418728
Med Oncol. 2013;30(3):686
pubmed: 23943423
Cancer Med. 2022 Sep;11(17):3226-3237
pubmed: 35322575
Onkologie. 2010;33(5):231-8
pubmed: 20502057
Neoplasma. 2018 Nov 15;65(6):972-979
pubmed: 30334450
Histopathology. 2018 Jul;73(1):19-28
pubmed: 29464758
Am J Pathol. 2002 Dec;161(6):1961-71
pubmed: 12466110
Cancer Lett. 2015 Jun 28;362(1):116-21
pubmed: 25813404
Thorac Cancer. 2019 Jan;10(1):47-53
pubmed: 30468296