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Development of a novel ALK rearrangement screening test for non–small cell lung cancers
Approximately 5–7% of non–small cell lung cancer (NSCLC) cases harbor an anaplastic lymphoma kinase (ALK) fusion gene and may benefit from ALK inhibitor therapy. To detect ALK fusion genes, we developed a novel test using reverse transcription polymerase chain reaction (RT-PCR) for the ALK kinase do...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462717/ https://www.ncbi.nlm.nih.gov/pubmed/34559836 http://dx.doi.org/10.1371/journal.pone.0257152 |
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author | Chen, Yi-Lin Chen, Wan-Li Cheng, Yi-Chia Lin, Ming-Ching Yang, Shu-Ching Tsai, Hung-Wen Lin, Chien‐Chung Su, Wu-Chou Chow, Nan-Haw Ho, Chung-Liang |
author_facet | Chen, Yi-Lin Chen, Wan-Li Cheng, Yi-Chia Lin, Ming-Ching Yang, Shu-Ching Tsai, Hung-Wen Lin, Chien‐Chung Su, Wu-Chou Chow, Nan-Haw Ho, Chung-Liang |
author_sort | Chen, Yi-Lin |
collection | PubMed |
description | Approximately 5–7% of non–small cell lung cancer (NSCLC) cases harbor an anaplastic lymphoma kinase (ALK) fusion gene and may benefit from ALK inhibitor therapy. To detect ALK fusion genes, we developed a novel test using reverse transcription polymerase chain reaction (RT-PCR) for the ALK kinase domain (KD). Since ALK expression is mostly silenced in the adult with the exception of neuronal tissue, the normal lung tissue, mesothelial lining, and inflammatory cells are devoid of ALK transcript, making ALK KD RT-PCR an ideal surrogate test for ALK fusion transcripts in lung or pleural effusion. The test was designed with a short PCR product (197 bp) to work for both malignant pleural effusion (MPE) and formalin-fixed, paraffin-embedded (FFPE) NSCLC samples. Using ALK IHC as a reference, the sensitivity of the test was 100% for both MPE and FFPE. The specificity was 97.6% for MPE and 97.4% for FFPE. Two false positive cases were found. One was a metastatic brain lesion which should be avoided in the future due to intrinsic ALK expression in the neuronal tissue. The other one resulted from ALK gene amplification. Due to potential false positivity, subsequent confirmation tests such as fluorescence in situ hybridization or multiplex PCR would be preferable. Nevertheless, the test is simple and inexpensive with no false negativity, making it a desirable screening test. It also offers an advantage over multiplex RT-PCR with the capability to detect novel ALK fusions. Indeed through the screening test, we found a novel ALK fusion partner (sperm antigen with calponin homology and coiled-coil domains 1 like gene, SPECC1L) with increased sensitivity to crizotinib in vitro. In summary, a novel RNA-based ALK KD analysis was developed for ALK rearrangement screening in MPE and FFPE specimens of NSCLC. This simple inexpensive test can be implemented as routine diagnostics. |
format | Online Article Text |
id | pubmed-8462717 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-84627172021-09-25 Development of a novel ALK rearrangement screening test for non–small cell lung cancers Chen, Yi-Lin Chen, Wan-Li Cheng, Yi-Chia Lin, Ming-Ching Yang, Shu-Ching Tsai, Hung-Wen Lin, Chien‐Chung Su, Wu-Chou Chow, Nan-Haw Ho, Chung-Liang PLoS One Research Article Approximately 5–7% of non–small cell lung cancer (NSCLC) cases harbor an anaplastic lymphoma kinase (ALK) fusion gene and may benefit from ALK inhibitor therapy. To detect ALK fusion genes, we developed a novel test using reverse transcription polymerase chain reaction (RT-PCR) for the ALK kinase domain (KD). Since ALK expression is mostly silenced in the adult with the exception of neuronal tissue, the normal lung tissue, mesothelial lining, and inflammatory cells are devoid of ALK transcript, making ALK KD RT-PCR an ideal surrogate test for ALK fusion transcripts in lung or pleural effusion. The test was designed with a short PCR product (197 bp) to work for both malignant pleural effusion (MPE) and formalin-fixed, paraffin-embedded (FFPE) NSCLC samples. Using ALK IHC as a reference, the sensitivity of the test was 100% for both MPE and FFPE. The specificity was 97.6% for MPE and 97.4% for FFPE. Two false positive cases were found. One was a metastatic brain lesion which should be avoided in the future due to intrinsic ALK expression in the neuronal tissue. The other one resulted from ALK gene amplification. Due to potential false positivity, subsequent confirmation tests such as fluorescence in situ hybridization or multiplex PCR would be preferable. Nevertheless, the test is simple and inexpensive with no false negativity, making it a desirable screening test. It also offers an advantage over multiplex RT-PCR with the capability to detect novel ALK fusions. Indeed through the screening test, we found a novel ALK fusion partner (sperm antigen with calponin homology and coiled-coil domains 1 like gene, SPECC1L) with increased sensitivity to crizotinib in vitro. In summary, a novel RNA-based ALK KD analysis was developed for ALK rearrangement screening in MPE and FFPE specimens of NSCLC. This simple inexpensive test can be implemented as routine diagnostics. Public Library of Science 2021-09-24 /pmc/articles/PMC8462717/ /pubmed/34559836 http://dx.doi.org/10.1371/journal.pone.0257152 Text en © 2021 Chen et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Chen, Yi-Lin Chen, Wan-Li Cheng, Yi-Chia Lin, Ming-Ching Yang, Shu-Ching Tsai, Hung-Wen Lin, Chien‐Chung Su, Wu-Chou Chow, Nan-Haw Ho, Chung-Liang Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title | Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title_full | Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title_fullStr | Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title_full_unstemmed | Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title_short | Development of a novel ALK rearrangement screening test for non–small cell lung cancers |
title_sort | development of a novel alk rearrangement screening test for non–small cell lung cancers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462717/ https://www.ncbi.nlm.nih.gov/pubmed/34559836 http://dx.doi.org/10.1371/journal.pone.0257152 |
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