Abstract 1541: Co-mutations define major subsets of KRAS-driven lung adenocarcinoma with implications for targeted cancer therapy
Authors: Skoulidis Ferdinandos , Coombes Kevin R. , Diao Lixia , Tong Pan , Cortez Maria A. , Giri Uma , Yang Chao , Fan You Hong , Weinstein John N. , Papadimitrakopoulou Vassiliki , Minna John D. , Wang Jing , Byers Lauren A. , Heymach John V. 
Published: May 2015

Introduction

The molecular underpinnings that beget the considerable biological and clinical heterogeneity of lung adenocarcinoma (AC) driven by oncogenic KRAS are poorly characterized. We hypothesized that significantly co-occurring mutations in components of key cellular tumor suppressor pathways are major determinants of signalling diversification downstream of mutant KRAS.

Methods

We applied un-supervised hierarchical analysis and classical multi-dimensional scaling to determine patterns of somatic (co)-mutations within a curated set of significantly mutated genes (MutSigCV p value &lt;0.001) among 99 KRAS-mutant lung ACs from the TCGA dataset. Independently, we derived expression clusters by applying un-supervised hierarchical analysis to a subset of 68 KRAS-driven lung ACs with available RNASeq data. Non-negative matrix factorization (NMF) was used to determine cluster stability.

Results

Clustering of KRAS-driven lung ACs based on patterns of somatic mutations revealed six major mutation clades. Five clades could be defined by combinations of somatic mutations in only four genes : KRAS, TP53, STK11/LKB1 and KEAP1, whereas a sixth clade appeared more heterogenous and was associated with a higher overall rate of somatic mutation.

Co-mutations in STK11/LKB1 and TP53 accounted for higher branches of the cluster dendrogram and were largely non-overlapping in the context of early-stage disease.

Integration of co-mutation analysis with unsupervised hierarchical analysis of RNA Seq differential expression data identified 3 major expression clusters, that were significantly enriched for the KRAS;TP53 (KP), KRAS;LKB1 (KL) and KRAS only (K) somatic mutation clades, as well as sub-clusters characterized by the presence of mutations in KEAP1. On the contrary, the distribution of the main KRAS amino acid substitutions (G12C, G12V and G12D) did not differ significantly between the expression clusters, indicating that co-mutations rather than distinct KRAS codon 12 base substitutions are the major driver of biological heterogeneity within KRAS-mutant lung ACs.

Re-analysis of publicly available large scale drug sensitivity data based on the proposed sub-classification revealed novel genotype-specific therapeutic vulnerabilities for the KL and KP subgroups including selective sensitivity of KL AC cell lines to MK-2206 ( a pan-AKT inhibitor), BX-795 (a PDK1 and TBK1/IKKϵ inhibitor) and the type II topoisomerase inhibitor etoposide. Selected hits were subsequently validated using pairs of isogenic cell lines.

Conclusions

Co-mutations in a small number of key tumor suppressor genes define biologically distinct and therapeutically relevant subgroups of KRAS-driven lung AC. Efforts to target KRAS signalling in the context of specific co-mutations may provide a more rational and personalized approach to therapy for this challenging group of lung cancer patients.

Citation Format: Ferdinandos Skoulidis, Kevin R. Coombes, Lixia Diao, Pan Tong, Maria A. Cortez, Uma Giri, Chao Yang, You Hong Fan, John N. Weinstein, Vassiliki Papadimitrakopoulou, John D. Minna, Jing Wang, Lauren A. Byers, John V. Heymach. Co-mutations define major subsets of KRAS-driven lung adenocarcinoma with implications for targeted cancer therapy. [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 1541. doi:10.1158/1538-7445.AM2014-1541