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...

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Autores principales:	Yi-Lin Chen, Wan-Li Chen, Yi-Chia Cheng, Ming-Ching Lin, Shu-Ching Yang, Hung-Wen Tsai, Chien-Chung Lin, Wu-Chou Su, Nan-Haw Chow, Chung-Liang Ho
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f237227974f540cd9dec0686f2f84839
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spelling	oai:doaj.org-article:f237227974f540cd9dec0686f2f848392021-12-02T20:08:00ZDevelopment of a novel ALK rearrangement screening test for non-small cell lung cancers.1932-620310.1371/journal.pone.0257152https://doaj.org/article/f237227974f540cd9dec0686f2f848392021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0257152https://doaj.org/toc/1932-6203Approximately 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.Yi-Lin ChenWan-Li ChenYi-Chia ChengMing-Ching LinShu-Ching YangHung-Wen TsaiChien-Chung LinWu-Chou SuNan-Haw ChowChung-Liang HoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0257152 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yi-Lin Chen Wan-Li Chen Yi-Chia Cheng Ming-Ching Lin Shu-Ching Yang Hung-Wen Tsai Chien-Chung Lin Wu-Chou Su Nan-Haw Chow Chung-Liang Ho Development of a novel ALK rearrangement screening test for non-small cell lung cancers.
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	article
author	Yi-Lin Chen Wan-Li Chen Yi-Chia Cheng Ming-Ching Lin Shu-Ching Yang Hung-Wen Tsai Chien-Chung Lin Wu-Chou Su Nan-Haw Chow Chung-Liang Ho
author_facet	Yi-Lin Chen Wan-Li Chen Yi-Chia Cheng Ming-Ching Lin Shu-Ching Yang Hung-Wen Tsai Chien-Chung Lin Wu-Chou Su Nan-Haw Chow Chung-Liang Ho
author_sort	Yi-Lin Chen
title	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_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_sort	development of a novel alk rearrangement screening test for non-small cell lung cancers.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/f237227974f540cd9dec0686f2f84839
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Development of a novel ALK rearrangement screening test for non-small cell lung cancers.

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