Assessment of ALK gene fusions in lung cancer using the differential expression and exon integrity methods

Abstract

Abstract. Anaplastic lymphoma kinase (ALK) gene fusion is a driving mutation underlying the development of non-small cell lung cancer (NSCLC). Accurate detection of ALK fusion is critical for the use of ALK inhibitors in the treatment of NSCLC. Commonly utilized methods for ALK detection include fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC). However, these methods are time-consuming and costly. In the present study, a method for assessing ALK gene fusion based on the differential expression levels of the ALK kinase and non-kinase domains was developed and evaluated, with the aim of providing a convenient and reliable method for the detection of ALK fusion. In addition, another method was established to determine the integrity of exons 19-20 and 20-21 of ALK, two genomic loci that are typically broken in ALK fusions. These novel methods were applied to detect ALK fusion in 100 NSCLC patients, and were compared with IHC and FISH methods. The novel methods developed in the present study successfully detected ALK fusions in 10 samples. The concordances between the novel methods and IHC and FISH were 100%. Furthermore, the differential expression method was able to detect ALK fusions in cell-free urine samples, which was advantageous over FISH and IHC. The novel methods developed in the present study are cost-effective and easy to perform, and may provide simple and convenient techniques for the clinical assessment of ALK fusions, facilitating the use of targeted therapy for NSCLC.

Molecular characterization of genomic breakpoints of ALK rearrangements in non‐small cell lung cancer

“…Notably, although lacking the 5′ acceptor splice site of ALK exon 20, the actual transcript of case #P2008280124 excluded partial nucleotides and retained a portion of exon 20 through an alternative splicing signal at the RNA level rather than implementing exon skipping splicing and it resulted in two different variants (E19; del14A20 and E19; del20A20). Further comparative analysis of the transcripts and the amino acid sequences showed that partial retention of exon 20 could ensure the in‐frame sequence with integrity of the ALK kinase domain [ 43 , 44 ]. Patients harbouring multiple EML4‐ALK variants implied a poor prognosis due to the high heterogeneity in the tumour tissue [ 45 ].…”

Aberrant expression of anaplastic lymphoma kinase in lung adenocarcinoma: Analysis of circulating free tumor RNA using one-step reverse transcription-polymerase chain reaction

“…However, the clinical application of specific RT-PCR assays has been limited by the number of reactions and the large quantity of clinical samples required to investigate the different ALK fusions. Previously, Huang et al (23) demonstrated, both on NSCLC tissue samples and on cell-free urine samples, the efficacy of a differential expression method, based on the presence of aberrant high levels of the ALK kinase domain (23). Notably, the predominant pathological consequence of ALK fusion in tumor cells is its aberrant expression, regardless of the fusion partner.…”