Abstract 2726: RET fusions identified in colorectal cancer PDX models are sensitive to the potent RET inhibitor ponatinib
Authors: Gozgit Joe M. , Chen Tzu-Hsiu , Clackson Tim , Rivera Victor M. 
Published: May 2015

Abstract
Background: Chromosomal translocations resulting in formation of activating RET fusion genes have been identified in papillary thyroid cancer and 1-2% of NSCLC. We have previously shown that ponatinib, a pan-BCR-ABL and multi-targeted tyrosine kinase inhibitor (TKI), potently inhibits the most common NSCLC fusion variant, KIF5B-RET, at clinically-achievable concentrations. Here we used patient-derived (PDX) tumor models to explore the potential involvement of RET fusions, and the efficacy of ponatinib, in other cancers.
Results: To identify potential RET fusion-positive PDX tumor models, we examined RET mRNA levels in 273 PDX tumors (Crown Bioscience) from various cancer types, looking for models with outlier RET expression. To search for RET fusions, we performed RNAseq on 4 tumors that had the highest RET levels. Interestingly, RET fusions were detected in tumors from 2 colorectal cancer (CRC) patients (pts) and not in tumors from 2 NSCLC pts that expressed similar levels of RET. The fusions detected in CRC pts, NCOA4-RET and CCDC6-RET, had previously been observed in NSCLC pts. Both CRC tumors were negative for other major hotspot mutations, including KRAS, BRAF and PI3K, suggesting that these RET-fusions might be primary oncogenic drivers in these tumors. To evaluate the cellular activity of ponatinib, we generated cell lines that were dependent on the activity of these fusions. Ponatinib potently inhibited the viability of Ba/F3 cells expressing NCOA4-RET and CCD6-RET with IC50s of 6 and 22 nM, respectively. Consistent with these effects being due to inhibition of RET, ponatinib inhibited RET phosphorylation with similar potency. Other TKIs with RET activity, vandetanib (IC50s: 564-1000 nM), cabozantinib (60-386 nM), sunitinib (277-584 nM), sorafenib (105-494 nM), and lenvatinib (68-257 nM), also inhibited viability of the Ba/F3 lines, but with potencies substantially reduced compared to ponatinib. Finally, we examined the efficacy of ponatinib in the RET fusion positive PDX colorectal models, compared to 2 RET fusion negative colorectal models. In the RET-negative models, daily oral dosing of ponatinib (20 mg/kg) inhibited tumor growth by 24-41%. In contrast, ponatinib exhibited much greater efficacy in the RET-fusion positive models, inhibiting tumor growth by 79% in the NCOA4-RET model and inducing near complete regression in the CCDC6-RET model.
Conclusion: We identified, for the first time, oncogenic RET fusions in CRC patient samples, suggesting RET may be a driver in a subset of CRC patients. Ponatinib effectively inhibited these fusions with potency substantially exceeding that of other RET inhibitors and demonstrated significant anti-tumor activity in PDX models. These results provide strong support for the clinical evaluation of ponatinib in patients with RET-fusion positive cancers, including colorectal cancer.
Citation Format: Joe M. Gozgit, Tzu-Hsiu Chen, Tim Clackson, Victor M. Rivera. RET fusions identified in colorectal cancer PDX models are sensitive to the potent RET inhibitor ponatinib. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2726. doi:10.1158/1538-7445.AM2014-2726