Abstract 5238: CLIP1-LTK: A novel druggable gene fusion in non-small cell lung cancer

Abstract Background: The discovery of oncogenic driver has uncovered the pathogenesis of non-small cell lung cancer (NSCLC), and development of corresponding kinase inhibitors has changed treatment strategies and improved survival of patients with druggable oncogenic drivers. However, no targeted therapies have been developed for the large proportion of advanced NSCLC. We established a multi-institutional lung cancer genome screening platform (LC-SCRUM-Asia) to identify lung cancer patients with oncogenic drivers and to clinically develop molecular-targeted therapies. Here, we apply this platform to search for novel druggable oncogenic drivers in NSCLC. Methods: We performed transcriptome sequencing of non-squamous NSCLC samples negative for known oncogenic drivers in the LC-SCRUM-Asia cohort. The presence of gene fusion was validated by RT-PCR, LTK break-apart fluorescence in situ hybridization (FISH). Sanger sequencing of gDNA and cDNA was performed to verify the breakpoint of these genes. The ability of oncogenic transformation was evaluated using NIH3T3 and Ba/F3 cell models in vitro and in vivo. The efficacy of seven compounds developed as ALK tyrosine kinase inhibitors (alectinib, brigatinib, ceritinib, crizotinib, entrectinib, lorlatinib, repotrectinib) were assessed. Results: Of consecutive 75 samples analyzed, we identified a novel in-frame fusion transcript of CLIP1 and LTK in a Japanese woman with lung adenocarcinoma. RT-PCR and LTK break apart FISH analyses confirmed the presence of LTK fusion and rearrangement, respectively, in this individual. Sanger sequencing verified the breakpoint in CLIP1 intron16 and LTK exon10, resulting in fusion sequence of CLIP1 exon16 to LTK exon11 in the expressed transcript. We show that kinase activity of CLIP1-LTK fusion protein is constitutively activated, along with phosphorylation of AKT and ERK, downstream of CLIP1-LTK, and has transformation potential dependent on LTK kinase activity. Treatment of Ba/F3 cells expressing CLIP1-LTK with lorlatinib, an ALK inhibitor, inhibited phosphorylation of CLIP1-LTK, AKT, and ERK, suppressed proliferation, and induced apoptosis. Conclusion: We identified the CLIP1-LTK fusion as a novel oncogenic driver in NSCLC, and the fusion protein can be targeted by lorlatinib. Urgent clinical development of molecular targeted agents and companion diagnostics for this new oncogenic driver are now warranted. Citation Format: Hiroki Izumi, Shingo Matsumoto, Jie Liu, Kosuke Tanaka, Shunta Mori, Shogo Kumagai, Takuma Hayashida, Yuji Shibata, Saori Takata, Eriko Tabata, Haruyasu Murakami, Reiko Taki, Satoshi Hara, Tomohiro Sakamoto, Koichi Goto, Susumu S. Kobayashi. CLIP1-LTK: A novel druggable gene fusion in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5238.