Clinically Viable Gene Expression Assays with Potential for Predicting Benefit from MEK Inhibitors.

Abstract

<b>Purpose:</b> To develop a clinically viable gene expression assay to measure RAS/RAF/MEK/ERK (RAS-ERK) pathway output suitable for hypothesis testing in non-small cell lung cancer (NSCLC) clinical studies.<b>Experimental Design:</b> A published MEK functional activation signature (MEK signature) that measures RAS-ERK functional output was optimized for NSCLC <i>in silico</i> NanoString assays were developed for the NSCLC optimized MEK signature and the 147-gene RAS signature. First, platform transfer from Affymetrix to NanoString, and signature modulation following treatment with <i>KRAS</i> siRNA and MEK inhibitor, were investigated in cell lines. Second, the association of the signatures with <i>KRAS</i> mutation status, dynamic range, technical reproducibility, and spatial and temporal variation was investigated in NSCLC formalin-fixed paraffin-embedded tissue (FFPET) samples.<b>Results:</b> We observed a strong cross-platform correlation and modulation of signatures <i>in vitro</i> Technical and biological replicates showed consistent signature scores that were robust to variation in input total RNA; conservation of scores between primary and metastatic tumor was statistically significant. There were statistically significant associations between high MEK (<i>P</i> = 0.028) and RAS (<i>P</i> = 0.003) signature scores and <i>KRAS</i> mutation in 50 NSCLC samples. The signatures identify overlapping but distinct candidate patient populations from each other and from <i>KRAS</i> mutation testing.<b>Conclusions:</b> We developed a technically and biologically robust NanoString gene expression assay of MEK pathway output, compatible with the quantities of FFPET routinely available. The gene signatures identified a different patient population for MEK inhibitor treatment compared with <i>KRAS</i> mutation testing. The predictive power of the MEK signature should be studied further in clinical trials. <i>Clin Cancer Res; 23(6); 1471-80. ©2016 AACR</i><i>See related commentary by Xue and Lito, p. 1365</i>.