Identification, functional study and clinical application of novel ALK fusion genes

Abstract

The fusion gene between echinoderm microtubule associated protein like 4 (EML4) and anaplastic lymphoma kinase (ALK) has been identified as a new molecular target of non small cell lung cancers (NSCLC). Recent clinical trials have reported remarkable clinical response (>80%) of NSCLC patients harboring EML4-ALK translocations to ALK inhibitors. Thus, elucidation of the biological functions of EML4;ALK or novel ALK fusion variants and their correlation with clinical characteristics may shed light on innovative treatment strategy for NSCLC. Approximately 5-7% of NSCLC patients harbor ALK fusion genes are sensitive to crizotinib. Currently, several technologies to delineate the ALK status are available, including immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) and reverse transcriptase-polymerase chain reaction (RT-PCR). However, there is no unanimous concordance among these technologies in the analysis of ALK status on formalin-fixed, paraffin-embedded (FFPE) material. In our prior study, a total of 13 FFPE specimens of NSCLC with ALK IHC (+) and wild type EGFR were investigated by break-apart FISH and RT-PCR. The ALK rearrangement status was almost consistent among 3 methods. The overall concordance between FISH and RT-PCR was over 90%. We noticed an ALK-positive case analyzed by IHC and FISH, but not by multiplex PCR. The 5'-RACE analysis together with sequencing of this case revealed a novel ALK fusion gene-SPECC1-ALK. The aim of this proposal is to examine the ALK transcripts and its 10 different partner genes in FFPE material by multiplex PCR in a clinical cohort. The results will be correlated with patients' outcome and response to targeting therapy. Then, biological effects of SPECC1-ALK expression in vitro and the associated signaling events will be investigated and to establish a cost-effective and sensitive ALK transcripts screening platform for molecular pathology laboratory.