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

Purpose: 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.Experimental Design: A published MEK functional activation signature (MEK signature) that measures RAS-ERK functional output was optimized for NSCLC in silico 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 KRAS siRNA and MEK inhibitor, were investigated in cell lines. Second, the association of the signatures with KRAS mutation status, dynamic range, technical reproducibility, and spatial and temporal variation was investigated in NSCLC formalin-fixed paraffin-embedded tissue (FFPET) samples.Results: We observed a strong cross-platform correlation and modulation of signatures in vitro 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 (P = 0.028) and RAS (P = 0.003) signature scores and KRAS mutation in 50 NSCLC samples. The signatures identify overlapping but distinct candidate patient populations from each other and from KRAS mutation testing.Conclusions: 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 KRAS mutation testing. The predictive power of the MEK signature should be studied further in clinical trials. Clin Cancer Res; 23(6); 1471-80. ©2016 AACRSee related commentary by Xue and Lito, p. 1365.

Patient Characteristics are not Associated with Clinically Important Differential Response to Dapagliflozin: a Staged Analysis of Phase 3 Data.

INTRODUCTION: This study aimed to determine if data mining methodologies could identify reproducible predictors of dapagliflozin-specific treatment response in the phase 3 clinical program dataset. METHODS: Baseline and early treatment response variables were selected and data mining used to identify/rank all variables associated with reduction in glycated hemoglobin (HbA1c) at week 26. Generalized linear modeling was then employed using an independent dataset to identify which (if any) variables were predictive of dapagliflozin-specific treatment response as compared with treatment response in the study's control arm. The most parsimonious (i.e., simplest) model was validated by meta-analysis of nine other trials. This staged approach was used to minimize risk of type I errors. RESULTS: From the large dataset, 22 variables were selected for model generation as potentially predictive for dapagliflozin-specific reduction in HbA1c. Although baseline HbA1c was the variable most strongly associated with reduction in HbA1c at study end (i.e., the best prognostic variable), baseline fasting plasma glucose (FPG) was the only predictive dapagliflozin-specific variable in the model. Placebo-adjusted treatment effect of dapagliflozin plus metformin vs. metformin alone for change in HbA1c from baseline was -0.65% at the average baseline FPG of 192.3 mg/dL (10.7 mmol/L). This response changed by -0.32% for every SD [57.2 mg/dL (3.2 mmol/L)] increase in baseline FPG. Effect of baseline FPG was confirmed in the meta-analysis of nine studies, but the magnitude was smaller. No other variable was independently predictive of a dapagliflozin-specific reduction in HbA1c. CONCLUSIONS: This methodology successfully identified a reproducible baseline predictor of differential response to dapagliflozin. Although baseline FPG was shown to be a predictor, the effect size was not of sufficient magnitude to suggest clinical usefulness in identifying patients who would uniquely benefit from dapagliflozin treatment. The findings do support potential benefit for dapagliflozin treatment that is consistent with current recommended use.

Evaluation of an automatic segmentation algorithm for definition of head and neck organs at risk.

BACKGROUND: The accurate definition of organs at risk (OARs) is required to fully exploit the benefits of intensity-modulated radiotherapy (IMRT) for head and neck cancer. However, manual delineation is time-consuming and there is considerable inter-observer variability. This is pertinent as function-sparing and adaptive IMRT have increased the number and frequency of delineation of OARs. We evaluated accuracy and potential time-saving of Smart Probabilistic Image Contouring Engine (SPICE) automatic segmentation to define OARs for salivary-, swallowing- and cochlea-sparing IMRT. METHODS: Five clinicians recorded the time to delineate five organs at risk (parotid glands, submandibular glands, larynx, pharyngeal constrictor muscles and cochleae) for each of 10 CT scans. SPICE was then used to define these structures. The acceptability of SPICE contours was initially determined by visual inspection and the total time to modify them recorded per scan. The Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm created a reference standard from all clinician contours. Clinician, SPICE and modified contours were compared against STAPLE by the Dice similarity coefficient (DSC) and mean/maximum distance to agreement (DTA). RESULTS: For all investigated structures, SPICE contours were less accurate than manual contours. However, for parotid/submandibular glands they were acceptable (median DSC: 0.79/0.80; mean, maximum DTA: 1.5 mm, 14.8 mm/0.6 mm, 5.7 mm). Modified SPICE contours were also less accurate than manual contours. The utilisation of SPICE did not result in time-saving/improve efficiency. CONCLUSIONS: Improvements in accuracy of automatic segmentation for head and neck OARs would be worthwhile and are required before its routine clinical implementation.