Abstract 5388: RNA in situ detection and characterization of ALK rearrangement in NSCLC FFPE tissues
Authors: Li Na , Wu Shafei , Wang Mindy , Sun Hongzhe , Zhang Zhifu , Park Emily , Ma Xiao-Jun , Zeng Xuan , Monroe Robert 
Published: August 2018

Abstract
Anaplastic lymphoma kinase (ALK) rearrangements are involved in ~4-7% of non-small cell lung cancers (NSCLCs). About 80% of ALK rearrangements generate a fusion gene between EML4 and ALK, resulting in overexpression of the fusion protein and constitutive kinase activity. Due to the sensitivity of tumors harboring ALK rearrangements to crizotinib, the identification of these rearrangements is clinically important. In this study, we developed an RNAscope® RNA ISH assay to specifically detect ALK rearrangement leading to upregulation of the 3' region of the ALK gene encoding the kinase domain in FFPE tissues from NSCLC. Two ALK-specific probes targeting ALK exons 1-18 (Hs-ALK E1-E18) and exons 19-29 (Hs-ALK E19-29) were tested in seven NSCLC FFPE samples. In three FISH-confirmed ALK rearrangement positive NSCLC cases, no signal was detected with the Hs-ALK E1-E18 probe, as expected. However, the Hs-ALK E19-29 probe showed positive signals (score 1 or 2) in all three FISH-confirmed cases of NSCLC. Among four ALK rearrangement negative samples (FISH and IHC confirmed), two samples exhibited no positivity with either probe. The other two cases showed low positivity with both probes in parts of the tumors, presumably representing baseline ALK mRNA expression (see table). Our results demonstrate that RNAscope® is a reliable method for the detection of ALK rearrangements that lead to the upregulation of the exons encoding the ALK kinase domain. The RNAscope® assay is both sensitive and specific for the detection of ALK rearrangement in FFPE tissues. Furthermore, the method provides information on the spatial distribution and morphologic context of cells associated with ALK rearrangements in NSCLC.
RNAscope HD 2.5 Red assay result scoreRNAscope HD 2.5 Red assay result scoreRNAscope HD 2.5 Red assay result scoreRNAscope HD 2.5 Red assay result scoresample labelALK-FISHIHC ALK-D5F3probe-PPIB (positive control)probe-DapB (negative control)probe-Hs-ALK E1-E18Probe-Hs-ALK E19-29Pathologic DiagnosisAgeGender (M/F)1+N/A2001 (50%)Highly-moderately differentiated invasive mucinous lung adenocarcinoma77F2+N/A2002 (&gt;90%)Moderately-poorly differentiated lung adenocarcinoma32M3+N/A3002 (&gt;90%)Highly-moderately differentiated lung adenocarcinoma, partly mucinous adenocarcinoma49M4--3000Lepidic predominant lung adenocarcinoma58F5--4000Lepidic predominant lung adenocarcinoma63M6--400 (90%), 2(10%)0 (90%), 2(10%)Invasive lung adenocarcinoma (papillary and alveolar predominant, partly micropapillary)48M7--300 (98%), 2(2%)0 (98%), 2(2%)Invasive lung adenocarcinoma (alveolar and lepidic predominant)52M
Citation Format: Na Li, Shafei Wu, Mindy Wang, Hongzhe Sun, Zhifu Zhang, Emily Park, Xiao-Jun Ma, Xuan Zeng, Robert Monroe. RNA in situ detection and characterization of ALK rearrangement in NSCLC FFPE tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5388.