Abstract A21: Modeling of oncogenic chromosomal translocations of aggressive fusion-positive sarcomas by CRISPR-Cas9 genomic engineering

A prominent challenge in fusion-positive sarcoma research is that the oncogenic driver is typically a chimeric transcription factor. Although considered the disease-specific molecular drivers, these chimeric transcription factors remain challenging to target pharmacologically. An alternative approach is the elucidation of molecular pathways controlled by the oncogenic transcription factor, with the aim of identifying druggable targets.

However, many fusion-driven sarcomas have a paucity of suitable genetic models, with some lacking any patient-derived cell lines. In the situations where patient-derived cell lines are available, most have been passaged for decades, potentially adding further complexity and bias. Therefore, development of faithful model systems of oncogenic chromosomal translocations is of principal importance for these aggressive translocation-driven pediatric sarcomas.

Here, we describe a novel approach that combines CRISPR-Cas9 genomic editing technology, with homology-directed repair (HDR) to engineer, capture, and modulate the expression of chromosomal translocation products in a human cell line.

We have applied this approach to the genetic modeling of t(11;22)(q24;q12) and t(11;22)(p13;q12), translocation products of the EWSR1 gene and its 3 fusion partners FLI1 and WT1, present in Ewing's sarcoma and desmoplastic small round cell tumor, respectively. Our approach establishes an innovative platform for constructing isogenic and conditionally inducible biologically relevant models for a variety of sarcomas driven by chromosomal translocations.

Citation Format: Lee Spraggon, Luciano Martelotto, Julija Hmeljak, Tyler Hitchman, Jiang Wang, Lu Wang, Emily Slotkin, Pang-Dian Fan, Jorge Reis-Filho, Marc Ladanyi. Modeling of oncogenic chromosomal translocations of aggressive fusion-positive sarcomas by CRISPR-Cas9 genomic engineering [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A21.

Role of ERBB signaling in RET-rearranged lung cancer and contribution of EGFR amplification to cabozantinib resistance

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Background: Lung cancers driven by oncogenic RET fusions have lower response rates to targeted monotherapy such as cabozantinib (28%) relative to response rates typically observed in ALK- or ROS1- rearranged lung adenocarcinomas (60-80%). Methods: To identify targetable co-dependencies or cooperating pathways for RET fusion-positive lung cancers, we performed high-throughput chemical and genetic screens to find FDA-approved drugs or genes that when inhibited, would synergize with cabozantinib in RET fusion-positive lung cancer cell lines. In addition we performed NGS of a pair of pre-treatment and post-cabozantinib progression samples. Results: We identified EGFR siRNAs and anti-EGFR drugs as synergistic with cabozantinib. Combinations of drugs that target EGFR (cetuximab, afatinib, erlotinib, gefitinib, neratinib) and RET (cabozantinib, CEP-32496, lenvatinib, vandetanib) were more effective at reducing growth of RET cell lines than any single agent in vitro and in xenograft models. Cabozantinib treatment of RET fusion-positive cell lines inhibited EGFR and RET phosphorylation, an observation not seen in RET wild-type cell lines. Co-immunoprecipitation studies reveal that RET and EGFR interact. Ectopic expression of CCDC6-RET in NIH-3T3 or human bronchial epithelial cells resulted in upregulation of multiple ERBB receptors and ligands (not seen in a ROS1 fusion-positive cell line) and a concomitant increase in EGFR stability. Treatment with ERBB pathway ligands or overexpression of EGFR decreased sensitivity to cabozantinib in two RET fusion-positive cell lines. Finally, sequencing of a pair of pre-treatment and post-progression samples from a lung cancer patient treated with cabozantinib revealed acquired amplification of EGFR in the latter sample. Conclusions: Taken together, these results suggest that the tumorigenic potential of RET fusion oncogenes is dependent on deregulation of ERBB-activated pathways and that a combination of RET and EGFR drugs could be more effective in treating RET fusion-positive tumors. Moreover, amplification of EGFR is a potential driver of resistance to cabozantinib in RET-rearranged lung cancers.