Abstract 3702: Integrated genomic and proteomic analysis identifies PTEN loss and AKT/MTOR as drivers of resistance to MEK inhibitors in NSCLC cells
Authors: Xia Dianren , Byers Lauren Averett , Diao Lixia , Wang Jing , Lin Steven H. , Gibbons Don Lynn , Gold Kathryn Ann , Paul Juliane , Liu Ningshu , Heymach John V. 
Published: May 2015

MEK inhibitors (MEKi) are a class of drugs targeting MEK1/2 in the RAS/RAF/MEK/ERK pathway. Previous studies have shown that the existence of KRAS mutation sensitizes tumor cells to MEKi. However, clinical data suggest that KRAS alone is not an adequate biomarker to predict benefit of MEKi to lung cancer patients. To investigate the additional biomarkers for MEKi, we conducted integrated genomic and proteomic analysis employing non-small cell lung cancer cell (NSCLC) lines as models. Correlation analysis showed that in resistant cell lines AKT/MTOR pathway was more active, including higher levels of phosphorylated AKT, p70S6K, 4EBP1, and S6 in a group of 72 NSCLC cell lines. While PI3K protein level remained the same, PTEN expression was higher in sensitive cell lines compared to resistant cell lines. This result was confirmed by a panel of NSCLC cell lines using western blotting. PTEN expression is lost due to mutations in a few cell lines, which results in the activation of the AKT/MTOR pathway. We found that PTEN mutation was one of three mutations consistently associated with MEKi resistance besides CDKN2A and SMARCA4. Knockdown of PTEN in sensitive cells increased their resistance to MEKi refametinib, selumetinib, and trametinib. On the other hand, overexpression of PTEN in resistant cells increased their sensitivity to these MEKi, suggesting that basal PTEN expression level affects cell sensitivity to MEKi and may serve as a predictive biomarker of response. Proteomic profiling also showed that refametinib effectively inhibited the phosphorylation ERK and its downstream effectors p90RSK and STK11. Refametinib had minimal effect on PTEN expression, but increased AKT/MTOR pathway activation. While most of the members of the AKT/MTOR pathway remained unchanged in response to refametinib in both sensitive and resistant cells, S6 phosphorylation was more suppressed by refametinib in sensitive cells than resistant cells, which was further confirmed using western blotting in a panel of NSCLC cells, suggesting that S6 phosphorylation may serve as a biomarker for response to MEKi. To study the mechanisms of PTEN loss in resistant cells, methylation profiling identified a number of regions in PTEN promoter highly methylated. Intriguingly, methylation inhibitor decitabine altered PTEN expression in most of the resistant cells, but not in sensitive cells. microRNA profiling also discovered a group of microRNAs associated with PTEN expression, and how these microRNAs regulates PTEN expression is under study. Overall, we found that basal PTEN level is maintained higher in sensitive cells compared to resistant cells. Alteration of PTEN expression affects cell sensitivity to MEKi. Thus, basal PTEN level can serve as a predictive biomarker to MEKi and its effect may be through modulating downstream S6 activation.

Citation Format: Dianren Xia, Lauren Averett Byers, Lixia Diao, Jing Wang, Steven H. Lin, Don Lynn Gibbons, Kathryn Ann Gold, Juliane Paul, Ningshu Liu, John V. Heymach. Integrated genomic and proteomic analysis identifies PTEN loss and AKT/MTOR as drivers of resistance to MEK inhibitors in NSCLC cells. [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 3702. doi:10.1158/1538-7445.AM2014-3702