Abstract C018: Primary tumor data analysis reveals novel synthetic lethal dependencies between KRAS mutation and the spliceosome

Identification of mutation-specific targeted therapies is a critical challenge in precision medicine. Synthetic lethality provides the basis for an approach to identify new therapeutic targets for mutations that are difficult to target directly, since in synthetic lethal (SL) interactions, an alteration in one gene leads to dependency on a second gene. Neither alteration by itself is essential for survival, but together these alterations lead to cancer cell death. We previously developed a new computational method, Mining Synthetic Lethals (MiSL), that can infer relationships from primary human tumor genomic and transcriptomic data and enable the identification of SL interactions in the context of native human tumors. The underlying assumption of MiSL is that SL partners of a mutation will be selectively amplified or never deleted in primary tumor samples harboring the mutation. Here, we used MiSL to identify novel SL partners of KRAS mutations in lung cancer. KRAS activating mutations are highly prevalent in lung cancer and aside from early clinical data on a novel covalent inhibitor for KRAS G12C mutations, there is no reported treatment to date for patients with KRAS mutations. We applied MiSL to identify SL interactions with KRAS G12 mutations in non-small cell lung cancer (NSCLC) and identified 220 SL partner genes. Some of these genes were foreseeable dependencies, such as MAPK, growth factor and inflammatory signaling associated genes; while others were novel SL candidates and included genes associated with splicing. Since we have access to a splicing-modulating drug in preclinical development, sudemycin D6 (SD6) which targets SF3B1, a spliceosome subunit, we focused on testing the SF3B1 interactors identified by MiSL, SLU7 and SRRM2. To enable validation studies, we first verified KRAS growth dependency in a panel of NSCLC cell lines using siRNA knock-down (KD). Next, we tested siRNA KD of predicted MiSL candidates on growth of KRAS-dependent (H358 and H441 – KRAS mutant) and KRAS-independent (H2228 – KRAS WT) cell lines. We confirmed that the KD of SLU7 expression reduced viability of KRAS mutant (75 to 85% reduced) but not KRAS wild-type (WT) cells lines. Similar differential viability was also observed with siRNA KD of SF3B1. Pharmacological inhibition of SF3B1 using SD6 also demonstrated that KRAS mutant cell lines were more sensitive to SD6 compared to a KRAS WT line (>5-30x). Finally, we validated these findings in an in vivo tumor xenograft model by treating KRAS WT and KRAS mutant tumors with SD6 and showed that the KRAS mutant tumors were significantly more inhibited by SD6 than KRAS WT tumors. Studies are ongoing to further confirm the SL interaction in lung cancer cell lines that are isogenic except for the KRAS mutation. In conclusion, SL predictions based on primary KRAS G12 mutant tumors indicated that splicing modulation is a vulnerability of KRAS tumors. Finally, synthetic lethal targets identified by primary tumor data mining can provide new therapeutic targets for KRAS specific mutant cancers, which can lead to personalized treatment options for NSCLC cancer patients. Citation Format: Claire E Repellin, Puja Patel, Yihui Shi, Helena Gong, Leena Shewade, Thomas Webb, Lidia Sambucetti, Subarna Sinha. Primary tumor data analysis reveals novel synthetic lethal dependencies between KRAS mutation and the spliceosome [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C018. doi:10.1158/1535-7163.TARG-19-C018