Evaluating the effectiveness of <scp>RNA </scp><i>in‐situ</i> hybridization for detecting lung adenocarcinoma with anaplastic lymphoma kinase rearrangement

Nakajima, N.; Yoshizawa, Akihiko; Kondo, Kyoko; Rokutan‐Kurata, Mariyo; Hirata, Masahiro; Furuhata, Ayako; Saito, Shinji; Sonobe, Makoto; Menju, Toshi; Momose, Masanobu; Fujimoto, Masakazu; Date, Hiroshi; Haga, Hironori

doi:10.1111/his.13198

Cited by 16 publications

(11 citation statements)

References 38 publications

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“…The association between GATA6 expression and alterations in EGFR , KRAS , HER2 , BRAF , ALK and ROS1 was evaluated. Mutation analysis was reported in our previous studies …”

Section: Methodsmentioning

confidence: 94%

GATA6‐positive lung adenocarcinomas are associated with invasive mucinous adenocarcinoma morphology, hepatocyte nuclear factor 4α expression, and KRAS mutations

et al. 2018

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“…The association between GATA6 expression and alterations in EGFR , KRAS , HER2 , BRAF , ALK and ROS1 was evaluated. Mutation analysis was reported in our previous studies …”

Section: Methodsmentioning

confidence: 94%

GATA6‐positive lung adenocarcinomas are associated with invasive mucinous adenocarcinoma morphology, hepatocyte nuclear factor 4α expression, and KRAS mutations

et al. 2018

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“…While protein-based expression analysis by immunohistochemistry (IHC) is the gold standard in pathology laboratories, multiplex RNA-FISH is a promising new approach to decipher cellular heterogeneity in tumors (24, 25). This approach is as sensitive as IHC but lacks its limitations with respect to antibody specificity and sensitivity (26, 27). Indeed, multiplex RNA-FISH overcomes the issue of protein epitope variation or antigen retrieval by tiling probes for the target gene across the entire length of the mRNA.…”

Section: Discussionmentioning

confidence: 99%

Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III

Messinger

Dai

Stanland

et al. 2019

mBio

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Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral gene expression and host gene expression. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of immune-suppressed individuals. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs), serving as a model of these lymphomas. In previous studies, reports from our laboratory have described a temporal model for immortalization with an initial phase characterized by expression of Epstein-Barr nuclear antigens (EBNAs), high levels of c-Myc activity, and hyperproliferation in the absence of the latent membrane proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly NFκB-activating LMP1, defining latency III. However, LCLs express a broad distribution of LMP1 such that a subset of these cells express LMP1 at levels similar to those seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA sequencing (mRNA-Seq) on early EBV-infected latency IIb cells and latency III LCLs sorted by NFκB activity. We found that latency IIb transcriptomes clustered independently from latency III independently of NFκB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-fluorescencein situhybridization (RNA-FISH) targeting EBVEBNA2orLMP1and humanCCR7orMGST1. This report defines latency IIb as a bona fide latency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity.IMPORTANCEEBV is a ubiquitous pathogen, with >95% of adults harboring a life-long latent infection in memory B cells. In immunocompromised individuals, latent EBV infection can result in lymphoma. The established expression profile of these lymphomas is latency III, which includes expression of all latency genes. However, single-cell analysis of EBV latent gene expression in these lymphomas suggests heterogeneity where most cells express the transcription factor, EBNA2, and only a fraction of the cells express membrane protein LMP1. Our work describes an early phase after infection where the EBNAs are expressed without LMP1, called latency IIb. However, LMP1 levels within latency III vary widely, making these states hard to discriminate. This may have important implications for therapeutic responses. It is crucial to distinguish these states to understand the molecular pathogenesis of these lymphomas. Ultimately, better tools to understand the heterogeneity of these cancers will support more-efficacious therapies in the future.

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“…Finally, nanoString might provide additional information complementary to IHC and FISH. In situ hybridization with RNA has also been described for evaluation of the tissue expression of an ALK rearrangement [ 86 , 87 , 88 ]. In fact, the RNA ISH method (RNAscope) is a rapid technique, with quite easy handling, similar to IHC.…”

Section: Methods For Detection Of An Alk Rearramentioning

confidence: 99%

ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice

Hofman

2017

Cancers

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Patients with advanced-stage non-small cell lung carcinoma (NSCLC) harboring an ALK rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. Several increasingly effective ALK inhibitors are now available for treatment of patients. However, despite an initial favorable response to treatment, in most cases relapse or progression occurs due to resistance mechanisms mainly caused by mutations in the tyrosine kinase domain of ALK. The detection of an ALK rearrangement is pivotal and can be done using different methods, which have variable sensitivity and specificity depending, in particular, on the quality and quantity of the patient’s sample. This review will first highlight briefly some information regarding the pathobiology of an ALK rearrangement and the epidemiology of patients harboring this genomic alteration. The different methods used to detect an ALK rearrangement as well as their advantages and disadvantages will then be examined and algorithms proposed for detection in daily routine practice.

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Evaluating the effectiveness of RNA in‐situ hybridization for detecting lung adenocarcinoma with anaplastic lymphoma kinase rearrangement

Abstract: Our findings show that RNA ISH is useful for detecting ALK rearrangement with high sensitivity and specificity relative to conventional IHC/FISH tests. Thus, RNA ISH, which is an easy and rapid assay, could be an alternative method to IHC and FISH.

Cited by 16 publications

References 38 publications

GATA6‐positive lung adenocarcinomas are associated with invasive mucinous adenocarcinoma morphology, hepatocyte nuclear factor 4α expression, and KRAS mutations

GATA6‐positive lung adenocarcinomas are associated with invasive mucinous adenocarcinoma morphology, hepatocyte nuclear factor 4α expression, and KRAS mutations

Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III

ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice

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